General Data

RNA Type	mRNA
Original Source	Sci-ModoM
Transcript ID:	ENST00000249499
Gene ID:	ENSG00000128709
Gene Name:	HOXD9
Sequence (UNICHARACTER ENCODING)	AGUCGGUGGCUCGGGCGCCGGCGGGGAGCUGCUCGGCGGCGGЖCAGUGUAAUGUUGGGUGGGAGUGCGGGACGCCUCAAAAUGUCUUCCAGUGGCACCCUCAGCAACUACUACGUGGЖCUCGCUUAUAGGCCAUGAGGGCGACGAGGUGUUCGCGGCGCGCUUCGGGCCGCCGGGGCCAGGCGCGCAGGGCCGGCCUGCAGGUGUGGCUGAUGGCCCGGCCGCCACCGCCGCCGAGUUCGCCUCGUGUAGUUUUGCCCCCAGAUCGGCCGUGUUCUCUGCCUCGUGGUCCGCGGUGCCCUCCCAGCCCCCGGCAGCGGCGGCGAUGAGCGGCCUCUACCACCCGUACGUUCCCCCGCCGCCCCUGGCCGCCUCUGCCUCCGAGCCCGGCCGCUACGUGCGCUCCUGGAUGGAGCCGCUGCCCGGCUUCCCGGGCGGUGCGGGCGGUGGCGGUGGUGGUGGAGGCGGCGGUCCGGGCCGCGGUCCCAGCCCUGGCCCCAGCGGCCCAGCCAACGGGCGCCACUACGGGAUUAAGCCUGAAACCCGAGCGGCCCCGGCCCCCGCCACGGCCGCCUCCACCACCUCCUCCUCCUCCACUUCCUUAUCCUCCUCCUCCAAACGGЖCUGAGUGCUCCGUGGCCCGGGAGUCCCAGGGGAGCAGCGGCCCCGAGUUCUCGUGCAACUCGUUCCUGCAGGAGAAGGCGGCAGCGGCGACGGGGGGAACCGGGCCUGGGGCAGGGAUCGGGGCCGCGACUGGGACGGGCGGCUCGUCGGAGCCCUCAGCUUGCAGCGACCACCCGAUCCCAGGCUGUUCGCUGAAGGAGGAGGAGAAGCAGCAUUCGCAGCCGCAGCAGCAGCAACUUGACCCAAACAACCCCGCCGCGAACUGGAUCCACGCUCGCUCCACCCGGAAAAAGCGCUGUCCCUACACCAAAUACCAGACGCUUGAGCUGGAGAAAGAAUUCCUCUUCAACAUGUACCUCACCCGGGACCGGCGCUACGAGGUGGCCAGGAUUCUCAACCUAACAGAGAGЖCAGGUCAAAAUCUGGUUUCAGAACCGUAGGAUGAAAAUGAAAAAGAUGAGCAAGGAGAAAUGCCCCAAAGGAGЖCUGACCCGGCGCGGUGCUGGCGGGAGCGCUCAAGGGCAGCGGAUUUGUUGUUGUUGCUGUUUUCCUUUGUGGGUGUUUGGUGCUUGAUUUCCAGAAACUCUCCAGCGACUUGGЖCUUCUUCUUCUUUUUUUUUUUCUUUUUAGAUAGAAGUGЖCUGUGUGGUUGGUCUCUGAGGUAUUUGGGGGЖCUCUGUAUUUGCUCGUUUACGUGUUGGAAAAACCAAGUGGCUUUGGGGUUUCGCCCUAUCCCACUCCCUCUCUUUCCUGCUCCAUUGGUUCCUUAAGAAAUGCUAUAUUUUGUGAGUGCAAGCUGGCUUGGGGAGCCCUCUCUUGUGUAAAUGUCCCCCAUGUUUCUGAAAAGUGCUGUAGUUUAGUCCCCUCACCCCCAGCACUGCCCAAACAGGGGCCAAGUGCGCCCCAAUUCCAAGAAUGAAGGCAGAGCGACAACAGUGCGGACACCCCGGCUGCUAGCCCACGGUGAAGCCCGGCGGGGUUGCCCACCAGUUGCGAAAGCCCCCUUUCCUCAGGGAGCACGCGGGACCUCGGUGGAGAUCUCCAGUGAGGCUUAGAGGAGCCCAGGGCCUCGGGCGGGUUGGGGUUUGUCCUCAGUGCAUUGGACGCGCUGCUCUCUCCCCUGAAGGCUGGGCUCGCGUGGGCGGCCGCGGGUGGUGGCCCUCCCGGUUCCUGCCCGAGGACCAGUUGUAAAUGUUACUGCUUCCUACUAAUAAAUGCUGACCUGAUCAAAUGGAGCCCAGACGCUGGCCCUAAA
Sequence (SHORT NAMES ENCODING)	AGUCGGUGGCUCGGGCGCCGGCGGGGAGCUGCUCGGCGGCGGm6ACAGUGUAAUGUUGGGUGGGAGUGCGGGACGCCUCAAAAUGUCUUCCAGUGGCACCCUCAGCAACUACUACGUGGm6ACUCGCUUAUAGGCCAUGAGGGCGACGAGGUGUUCGCGGCGCGCUUCGGGCCGCCGGGGCCAGGCGCGCAGGGCCGGCCUGCAGGUGUGGCUGAUGGCCCGGCCGCCACCGCCGCCGAGUUCGCCUCGUGUAGUUUUGCCCCCAGAUCGGCCGUGUUCUCUGCCUCGUGGUCCGCGGUGCCCUCCCAGCCCCCGGCAGCGGCGGCGAUGAGCGGCCUCUACCACCCGUACGUUCCCCCGCCGCCCCUGGCCGCCUCUGCCUCCGAGCCCGGCCGCUACGUGCGCUCCUGGAUGGAGCCGCUGCCCGGCUUCCCGGGCGGUGCGGGCGGUGGCGGUGGUGGUGGAGGCGGCGGUCCGGGCCGCGGUCCCAGCCCUGGCCCCAGCGGCCCAGCCAACGGGCGCCACUACGGGAUUAAGCCUGAAACCCGAGCGGCCCCGGCCCCCGCCACGGCCGCCUCCACCACCUCCUCCUCCUCCACUUCCUUAUCCUCCUCCUCCAAACGGm6ACUGAGUGCUCCGUGGCCCGGGAGUCCCAGGGGAGCAGCGGCCCCGAGUUCUCGUGCAACUCGUUCCUGCAGGAGAAGGCGGCAGCGGCGACGGGGGGAACCGGGCCUGGGGCAGGGAUCGGGGCCGCGACUGGGACGGGCGGCUCGUCGGAGCCCUCAGCUUGCAGCGACCACCCGAUCCCAGGCUGUUCGCUGAAGGAGGAGGAGAAGCAGCAUUCGCAGCCGCAGCAGCAGCAACUUGACCCAAACAACCCCGCCGCGAACUGGAUCCACGCUCGCUCCACCCGGAAAAAGCGCUGUCCCUACACCAAAUACCAGACGCUUGAGCUGGAGAAAGAAUUCCUCUUCAACAUGUACCUCACCCGGGACCGGCGCUACGAGGUGGCCAGGAUUCUCAACCUAACAGAGAGm6ACAGGUCAAAAUCUGGUUUCAGAACCGUAGGAUGAAAAUGAAAAAGAUGAGCAAGGAGAAAUGCCCCAAAGGAGm6ACUGACCCGGCGCGGUGCUGGCGGGAGCGCUCAAGGGCAGCGGAUUUGUUGUUGUUGCUGUUUUCCUUUGUGGGUGUUUGGUGCUUGAUUUCCAGAAACUCUCCAGCGACUUGGm6ACUUCUUCUUCUUUUUUUUUUUCUUUUUAGAUAGAAGUGm6ACUGUGUGGUUGGUCUCUGAGGUAUUUGGGGGm6ACUCUGUAUUUGCUCGUUUACGUGUUGGAAAAACCAAGUGGCUUUGGGGUUUCGCCCUAUCCCACUCCCUCUCUUUCCUGCUCCAUUGGUUCCUUAAGAAAUGCUAUAUUUUGUGAGUGCAAGCUGGCUUGGGGAGCCCUCUCUUGUGUAAAUGUCCCCCAUGUUUCUGAAAAGUGCUGUAGUUUAGUCCCCUCACCCCCAGCACUGCCCAAACAGGGGCCAAGUGCGCCCCAAUUCCAAGAAUGAAGGCAGAGCGACAACAGUGCGGACACCCCGGCUGCUAGCCCACGGUGAAGCCCGGCGGGGUUGCCCACCAGUUGCGAAAGCCCCCUUUCCUCAGGGAGCACGCGGGACCUCGGUGGAGAUCUCCAGUGAGGCUUAGAGGAGCCCAGGGCCUCGGGCGGGUUGGGGUUUGUCCUCAGUGCAUUGGACGCGCUGCUCUCUCCCCUGAAGGCUGGGCUCGCGUGGGCGGCCGCGGGUGGUGGCCCUCCCGGUUCCUGCCCGAGGACCAGUUGUAAAUGUUACUGCUUCCUACUAAUAAAUGCUGACCUGAUCAAAUGGAGCCCAGACGCUGGCCCUAAA
Sequence (MODOMICS CODE ENCODING)	AGUCGGUGGCUCGGGCGCCGGCGGGGAGCUGCUCGGCGGCGG2000000006ACAGUGUAAUGUUGGGUGGGAGUGCGGGACGCCUCAAAAUGUCUUCCAGUGGCACCCUCAGCAACUACUACGUGG2000000006ACUCGCUUAUAGGCCAUGAGGGCGACGAGGUGUUCGCGGCGCGCUUCGGGCCGCCGGGGCCAGGCGCGCAGGGCCGGCCUGCAGGUGUGGCUGAUGGCCCGGCCGCCACCGCCGCCGAGUUCGCCUCGUGUAGUUUUGCCCCCAGAUCGGCCGUGUUCUCUGCCUCGUGGUCCGCGGUGCCCUCCCAGCCCCCGGCAGCGGCGGCGAUGAGCGGCCUCUACCACCCGUACGUUCCCCCGCCGCCCCUGGCCGCCUCUGCCUCCGAGCCCGGCCGCUACGUGCGCUCCUGGAUGGAGCCGCUGCCCGGCUUCCCGGGCGGUGCGGGCGGUGGCGGUGGUGGUGGAGGCGGCGGUCCGGGCCGCGGUCCCAGCCCUGGCCCCAGCGGCCCAGCCAACGGGCGCCACUACGGGAUUAAGCCUGAAACCCGAGCGGCCCCGGCCCCCGCCACGGCCGCCUCCACCACCUCCUCCUCCUCCACUUCCUUAUCCUCCUCCUCCAAACGG2000000006ACUGAGUGCUCCGUGGCCCGGGAGUCCCAGGGGAGCAGCGGCCCCGAGUUCUCGUGCAACUCGUUCCUGCAGGAGAAGGCGGCAGCGGCGACGGGGGGAACCGGGCCUGGGGCAGGGAUCGGGGCCGCGACUGGGACGGGCGGCUCGUCGGAGCCCUCAGCUUGCAGCGACCACCCGAUCCCAGGCUGUUCGCUGAAGGAGGAGGAGAAGCAGCAUUCGCAGCCGCAGCAGCAGCAACUUGACCCAAACAACCCCGCCGCGAACUGGAUCCACGCUCGCUCCACCCGGAAAAAGCGCUGUCCCUACACCAAAUACCAGACGCUUGAGCUGGAGAAAGAAUUCCUCUUCAACAUGUACCUCACCCGGGACCGGCGCUACGAGGUGGCCAGGAUUCUCAACCUAACAGAGAG2000000006ACAGGUCAAAAUCUGGUUUCAGAACCGUAGGAUGAAAAUGAAAAAGAUGAGCAAGGAGAAAUGCCCCAAAGGAG2000000006ACUGACCCGGCGCGGUGCUGGCGGGAGCGCUCAAGGGCAGCGGAUUUGUUGUUGUUGCUGUUUUCCUUUGUGGGUGUUUGGUGCUUGAUUUCCAGAAACUCUCCAGCGACUUGG2000000006ACUUCUUCUUCUUUUUUUUUUUCUUUUUAGAUAGAAGUG2000000006ACUGUGUGGUUGGUCUCUGAGGUAUUUGGGGG2000000006ACUCUGUAUUUGCUCGUUUACGUGUUGGAAAAACCAAGUGGCUUUGGGGUUUCGCCCUAUCCCACUCCCUCUCUUUCCUGCUCCAUUGGUUCCUUAAGAAAUGCUAUAUUUUGUGAGUGCAAGCUGGCUUGGGGAGCCCUCUCUUGUGUAAAUGUCCCCCAUGUUUCUGAAAAGUGCUGUAGUUUAGUCCCCUCACCCCCAGCACUGCCCAAACAGGGGCCAAGUGCGCCCCAAUUCCAAGAAUGAAGGCAGAGCGACAACAGUGCGGACACCCCGGCUGCUAGCCCACGGUGAAGCCCGGCGGGGUUGCCCACCAGUUGCGAAAGCCCCCUUUCCUCAGGGAGCACGCGGGACCUCGGUGGAGAUCUCCAGUGAGGCUUAGAGGAGCCCAGGGCCUCGGGCGGGUUGGGGUUUGUCCUCAGUGCAUUGGACGCGCUGCUCUCUCCCCUGAAGGCUGGGCUCGCGUGGGCGGCCGCGGGUGGUGGCCCUCCCGGUUCCUGCCCGAGGACCAGUUGUAAAUGUUACUGCUUCCUACUAAUAAAUGCUGACCUGAUCAAAUGGAGCCCAGACGCUGGCCCUAAA

Score Table

_{Table containing the score explanation. Score identify the level of experimental reliability and evidence so as exaplained in the 2023 release manuscript. Class 1 should be considered as highlyrelevant. Class 2 evidences are considered as Solid, namely large errors are unlikely and minor errors should not undermine the meaning of data. Class 3 is considered as speculative and errors are expected. Class 4 is considered as questionable. Class 5 evidence means that verification and data are still to be collected. Class 6 data cannot be estimated.}

Method Classification	Score
Multiple direct experimental evidence	1
Direct experimental evidence	2
Inferred based on indirect experimental evidence	3
Predicted computationally	4
Evidence not yet annotated (Unknown)	5
Irrelevant	6

Modification Positions

_{Table containing the original modifications present in the MODOMICS sequences. Edit locations not originally present in the RNA sequences are marked by their source. Their scores are in third row.}

Position in the Sequence	43	118	621	1031	1105	1219	1258	1290
Modification Positions	m6A	m6A	m6A	m6A	m6A	m6A	m6A	m6A
Genomic Coordinates	2:176122761:+	2:176122836:+	2:176123339:+	2:176124097:+	2:176124171:+	2:176124285:+	2:176124324:+	2:176124356:+
Level of Experimental Evidence	3	3	3	3	3	3	3	3
Level of Experimental Reliability	3	3	3	3	3	3	3	3
Source	Sci-ModoM	Sci-ModoM	Sci-ModoM	Sci-ModoM	Sci-ModoM	Sci-ModoM	Sci-ModoM	Sci-ModoM
EUFIDs	4HMi5ykupT9V 6UuHp6YApVKv gBgcfFQ5WN9C gZuvgwMuBfgh jNkxUQNx8GRd Mg9GixDBFQAT msuJfBpJvM5H NjZ8bGGJsNSR Q36pf44ZRvxu UN3tNpbCPHYf VL7zkHvkfkoB VyCX26p5UBRL WdHxkJGRmFxn	3TeAZFYFxgvp 4HMi5ykupT9V 5Nnepx5V7yHo 6AyXsheySjfx 6UuHp6YApVKv aHkqKEJkRYyb aivdrAsbdKEU Ap2q43bQLNek gBgcfFQ5WN9C gZuvgwMuBfgh jNkxUQNx8GRd Mg9GixDBFQAT msuJfBpJvM5H nGifePrmgHfe NjZ8bGGJsNSR Q36pf44ZRvxu QmcpiJ88DBDn QpiKdbVikVz2 UN3tNpbCPHYf V5PvfiKsgFMd VL7zkHvkfkoB VyCX26p5UBRL WdHxkJGRmFxn	3TeAZFYFxgvp 5Nnepx5V7yHo 6AyXsheySjfx 6UuHp6YApVKv aHkqKEJkRYyb aivdrAsbdKEU Ap2q43bQLNek gBgcfFQ5WN9C gZuvgwMuBfgh jNkxUQNx8GRd Mg9GixDBFQAT msuJfBpJvM5H nGifePrmgHfe NjZ8bGGJsNSR Q36pf44ZRvxu QmcpiJ88DBDn QpiKdbVikVz2 UN3tNpbCPHYf V5PvfiKsgFMd VL7zkHvkfkoB VyCX26p5UBRL WdHxkJGRmFxn	3TeAZFYFxgvp 4HMi5ykupT9V 5aTkEfEpX8Xm 5Nnepx5V7yHo 6AyXsheySjfx 6UuHp6YApVKv aHkqKEJkRYyb aivdrAsbdKEU Ap2q43bQLNek gBgcfFQ5WN9C gZuvgwMuBfgh jNkxUQNx8GRd msuJfBpJvM5H nGifePrmgHfe NjZ8bGGJsNSR Q36pf44ZRvxu QmcpiJ88DBDn QpiKdbVikVz2 UN3tNpbCPHYf V5PvfiKsgFMd VL7zkHvkfkoB VyCX26p5UBRL WdHxkJGRmFxn Yfn77uLS5tv8	6UuHp6YApVKv aHkqKEJkRYyb aivdrAsbdKEU jNkxUQNx8GRd Mg9GixDBFQAT msuJfBpJvM5H nGifePrmgHfe Q36pf44ZRvxu QpiKdbVikVz2 UN3tNpbCPHYf VL7zkHvkfkoB VyCX26p5UBRL WdHxkJGRmFxn BkoLW2CBToyL Yfn77uLS5tv8	4HMi5ykupT9V 5aTkEfEpX8Xm 6UuHp6YApVKv gBgcfFQ5WN9C gZuvgwMuBfgh jNkxUQNx8GRd Mg9GixDBFQAT msuJfBpJvM5H nGifePrmgHfe V5PvfiKsgFMd VL7zkHvkfkoB VyCX26p5UBRL WdHxkJGRmFxn Lny8GcCeVGc9 Yfn77uLS5tv8	4HMi5ykupT9V 5aTkEfEpX8Xm 6AyXsheySjfx 6UuHp6YApVKv aHkqKEJkRYyb Ap2q43bQLNek jNkxUQNx8GRd msuJfBpJvM5H nGifePrmgHfe QmcpiJ88DBDn UN3tNpbCPHYf V5PvfiKsgFMd VL7zkHvkfkoB VyCX26p5UBRL WdHxkJGRmFxn UKen6WEino9G Yfn77uLS5tv8	3TeAZFYFxgvp 4HMi5ykupT9V 5aTkEfEpX8Xm 6AyXsheySjfx 6UuHp6YApVKv aivdrAsbdKEU Ap2q43bQLNek gBgcfFQ5WN9C gZuvgwMuBfgh jNkxUQNx8GRd Mg9GixDBFQAT msuJfBpJvM5H NjZ8bGGJsNSR Q36pf44ZRvxu QmcpiJ88DBDn UN3tNpbCPHYf V5PvfiKsgFMd VL7zkHvkfkoB VyCX26p5UBRL WdHxkJGRmFxn dknfVe6BK8aP Yfn77uLS5tv8