Sequence
atgc intronic sequence ATGC exonic sequence...tgtagattccatttggagctttccaatttttctttatatatctcctttgactatcagtaaccattgctatattcttgtttatttttaaaaccacattcagAGAAAAACTGGTGGTCTGGTGATTTGGAGGTCTGGCAACTCTGTTTCCTTATACAGGGGTGTGAGCTACGAGGTTCCTTCAGTACAACAGAATAAAAAAA
Basic information
species | Glycine max |
transcript | GLYMA20G34730.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34730.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G14510.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------------------------------tgtagattccat--ttggagctttccaatttttctttatatatctcctttgactatcagtaaccattgctatattcttgtttatttttaaaaccacatt----cagAGAAAAACTGGTGGTCTGGTGATTTGGAGGTCTGGCAACTCTGTTTCCTTATACAG------GGGTGTGAGCTACGAGGTTCCTTCAGTACAACAGAATAAAAAAA
|| | || |||||||||| ||| | | | | | || | | || | | | | ||| | | || | |||||||||||||||||| |||||||||||||||| || | || | |||| |||| |||| ||| || || | |||| | ||| |
gttttacttcttatgatcccccaatcagtgtttttatttacaaaggcttaatctttggagctttgaaatgatataagtcaaagaattgaaagttctttgtttctagtgtgtcaagtgtaatactaattatatcttcactgtgacagAGAAAAACTGGTGGTTTGGTGATTTGGAGGTCAGGGACTTCCATCGCCTTGTACAATTACAAAGGTGGCAGCAACAGGGATGGATCAGGGAACATGAACA------
upper sequence: GLYMA20G34730.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0020g04770.t01 (Vitis vinifera), 3'ss of exon 1
-tgtagattccatttggagctttccaattt--ttctttatatatctcctttgactatcagtaaccattgctatattcttgtttatttttaaaaccacattcagAGAAAAACTGGTGGTCTGGTGATTTGGAGGTCTGGCAACTCTGTTTCCTTATACAGGGGTGTGAGCTACGAGGTTCCTTCAGTACAACAGAATAAAAAAA---
|| ||| | | | | ||||| || || |||||| ||| | | | | ||| ||| || || | | | || | | |||||||||||||||||||| ||||||| ||||| ||||||| |||||||| |||| || ||||||||||| |||||||| ||| |||| ||| ||||
caatacattac-cctagtgaaaaagaatttggttgttaatatat-tccaataaatggctttaatcatctgtaagttgat-tctgccttctccattatgttcagAGAAAAACTGGTGGTTTGGTGATATGGAGATCTGGCACTTCTGTTTCTCTATATAGAGGTGTGAGCTATGAGGTTCC---AGTCCAACTGAACAAAAGGGTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgactatcagtaaccattgctatattcttgtttatttttaaaaccacattcagAGAAAAACTGGTGGTCTGGTGATTTGGAGGTCTGGCAACTCTGTTTCCTTATACAGGGGTGTGAGCTACGAGGTTCCTTCAGTACAACAGAATAAAAAAA
cagtaac putative branch site (score: 2)
attgctatattcttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtagattccatttggagctttccaatttttctttatatatctcctttgactatcagtaaccattgctatattcttgtttatttttaaaaccacattcagAGAAAAACTGGTGGTCTGGTGATTTGGAGGTCTGGCAACTCTGTTTCCTTATACAGGGGTGTGAGCTACGAGGTTCCTTCAGTACAACAGAATAAAAAAA
- - - - ccatttg
- - - - - - - - -gctttcc
- - - - - - - - - - - - - - - - - - - - - tcctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccattgc