Sequence
atgc intronic sequence ATGC exonic sequence...gtgatttgatgactttcagtttactttgtcactttttaaggttaaccaatagctttgcttatgtatatcttcatcctttctactatttgattactgtcagATGTGAAGGATGTGAAATATGTAATAAATTATGACTTCCGGGGGTCACTTGAGGATTATGTTCATCGCATTGGGCGGATAGGGAGAGCTGGCGCAAAAGG
Basic information
species | Glycine max |
transcript | GLYMA07G11880.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 8
gtgatttgatgactttcagtttactttgtcactttttaaggttaaccaat-agctttgcttatgtatatcttcatcctttctactatttgattactgtcagATGTGAAGGATGTGAAATATGTAATAAATTATGACTTCCGGGGGTCACTTGAGGATTATGTTCATCGCATTGGGCGGATAGGGAGAGCTGGCGCAAAAGG
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--------------------gtatacaaaaatcctcccagatcgatgaattatatttatttctgtaaac--taatgccactta-tatctggaaac----agATGTTAAGGATGTTAAATATGTCATTAACTATGACTTTCCGGGATCATTGGAGGATTATGTTCATCGCATTGGTCGAACTGGCAGAGCTGGAGCAAAAGG
upper sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 8
gtgatttgatgactttcagtttactttgtcactttttaaggt-taaccaatagctttgcttatgtatatcttcatcctttctactatttgattactgtcagATGTGAAGGATGTGAAATATGTAATAAATTATGACTTCCGGGGGTCACTTGAGGATTATGTTCATCGCATTGGGCGGATAGGGAGAGCTGGCGCAAAAGG
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-----------------------gtatgcccaactttgagatgtgatacatcttatatttcctgaggaaattgatacacgtttctttcccttggaaaacagATGTCAAGGATGTGAAGTATGTCATTAACTATGACTTTCCGGGGTCACTCGAGGATTATGTTCATCGTATAGGTCGAACTGGCAGAGCAGGTGCAAAAGG
upper sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgatttgatgactttcagtttactttgtcactttttaaggttaaccaatagctttgcttatgtatatcttcatcctttctactatttgattactgt----cagATGTGAAGGATGTGAAATATGTAATAAATTATGACTTCCGGGGGTCACTTGAGGATTATGTTCATCGCATTGGGCGGATAGGGAGAGCTGGCGCAAAAGG
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---------------gtactaaatctttttctcatctgcgtgcaaacatcaactct-cttaaccatggtgacaagctaacaacagttctttttgttttgaacagACGTGAAAGATGTGAAGTATGTGATAAACTATGACTTCCCTGGATCACTGGAGGATTATGTTCACAGGATTGGACGAACAGGTAGAGCCGGGGCTAAAGG
upper sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 8
gtgatttgatgactttcagtttactttgtcactttttaaggttaaccaatagctttgcttatgtatatcttcatcctttctac-tatttgattactgt--cagATGTGAAGGATGTGAAATATGTAATAAATTATGACTTCCGGGGGTCACTTGAGGATTATGTTCATCGCATTGGGCGGATAGGGAGAGCTGGCGCAAAAGG
||| || | ||| | || | | | | ||| | | | | | |||| ||| ||| | || | || || ||||||| ||||||||||||| ||| || || |||||||||| ||| || ||||| |||||||| || |||||||| || | ||| || ||||| || |||||
-tgacatggctaaattcttgaaaggaagtgagagcat--gtccacccaggatgacttcaaaagctgcatttcaatcttcttacatgttaggttttggttgcagATGTCAAGGATGTGAAATTTGTGATCAACTATGACTTCCCGGGATCTCTTGAAGATTATGTCCACCGCATTGGTCGAACAGGAAGGGCTGGGGCCAAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaatagctttgcttatgtatatcttcatcctttctactatttgattactgtcagATGTGAAGGATGTGAAATATGTAATAAATTATGACTTCCGGGGGTCACTTGAGGATTATGTTCATCGCATTGGGCGGATAGGGAGAGCTGGCGCAAAAGG
atttgat putative branch site (score: 5)
ttatgtatat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatttgatgactttcagtttactttgtcactttttaaggttaaccaatagctttgcttatgtatatcttcatcctttctactatttgattactgtcagATGTGAAGGATGTGAAATATGTAATAAATTATGACTTCCGGGGGTCACTTGAGGATTATGTTCATCGCATTGGGCGGATAGGGAGAGCTGGCGCAAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - tgatgac
- - - - - - - - - - - - - tgtcact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttatg