Sequence
atgc intronic sequence ATGC exonic sequencegtgtgctcacaatcctatagttctgtaaattgatgtacaaataattatgtcagacatgatggcttattttctttttggttgttgagttatgcagATGTCTGCTGATGATTTCATAAGAAACAATCGTGGCATTGATGATGGAAAAGATTTGCCAGAGGAATACTTGAGGTCCTTGTTTGAGAGAATATCTAGAA
Basic information
species | Glycine max |
transcript | GLYMA03G02610.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 4
gtgtgctcacaatcctatagttctgtaaattgatgtacaaataattatgtca-gacatgatggcttattt--tctttttggttgttgagttatgcagATGTCTGCTGATGATTTCATAAGAAACAATCGTGGCATTGATGATGGAAAAGATTTGCCAGAGGAATACTTGAGGTCCTTGTTTGAGAGAATATCTAGAA
||| || ||| | || | | | | ||| ||| | | | |||| ||||||||||| | || |||||||| |||||||||||||| || |||||||| || || | || || |||| |||| || |||| ||| || || | | ||
------------------------gtactttcttgtggtgaaggttcttttgcggagttctggtttacacaattatgtaacatgttactcgatgcagATGTCACCAGAAGATTTCATTAGAAACAATCGTGGTATCGATGATGGGAAGGACCTACCTGAAGAATTTATGAGATCATTGTATGAAAGGATTTGGAAAA
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 4
-----gtgtgctcacaatcct--atagttctgtaa--attgatgtacaaataattatgtcag--acatgatggcttattttctttttggttgttgagttatgcagATGTCTGCTGATGATTTCATAAGAAACAATCGTGGCATTGATGATGGAAAAGATTTGCCAGAGGAATACTTGAGGTCCTTGTTTGAGAGAATATCTAGAA
| ||| || ||| | | || | | || || | | |||| || || | | | ||| ||||| | ||| || |||||||||||||||| || || |||||||||||||| || || || ||||||||||| || | ||| ||| |||| || ||| ||| || ||| | |
gtttgcttcattcattgtctaggataatacagttattgtggaagttttaggtaaaatgttagtgacgttctttgtgcctttttttttttctcttggaacatatagATGTCTGCTGATGACTTTATCAGAAACAATCGTGGAATAGACGACGGAAAAGATTTACCTGCGGACTACATGAGATCGCTGTATGAAAGGATAACAAAGC
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------gtgtgctcacaatcctatagttctgtaaattgatgtacaaataattat--gtcagacatgatggcttatt-ttctttttggttgttgagttatgcagATGTCTGCTGATGATTTCATAAGAAACAATCGTGGCATTGATGATGGAAAAGATTTGCCAGAGGAATACTTGAGGTCCTTGTTTGAGAGAATATCTAGAA
| | ||| | | | | | | | | | || |||| ||| | || ||| | ||| || |||||||| | ||||||| ||| || |||||||||||||| || |||||||| ||||||||||| |||||||| | | | || | ||| || ||||||||||
gtacatatttgagctgtttcgcttagaagctttctgaaatccctcttgaggaatatcttaatacgatcttgtttgaagcttgtgattggtcaaacaaagtaactcattactaaatttttcaattacaacttgcagATGACAGCTGATGGTTTTATTAGAAACAATCGTGGTATAGATGATGGGAAAGATTTGCCTGAGGAATATCTACGTGCATTATATGAAAGGATATCTAGAA
upper sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 4
gtgtgctcacaatcctatagttctgtaaattgatgtacaa-ataattatgtcagacatgatggcttatt------ttctttttggttgttgagttatgcagATGTCTGCTGATGATTTCATAAGAAACAATCGTGGCATTGATGATGGAAAAGATTTGCCAGAGGAATACTTGAGGTCCTTGTTTGAGAGAATATCTAGAA
|| | |||| || || | || | ||||| || || || | | || | ||||| || |||||||| || | |||||||||||| |||||||||| |||||||||||||||||||| ||||| ||||||||||| || ||||| || |||| || |||| ||| | ||||| ||||
gtatactcaaaaatttaatttgaagttatgagatgtttaatatcataacttgctgaatttctgtttattattaatttttttttggtcattaaaatatgcagATGTCGCCTGATGATTTTATAAGAAACAATCGTGGCATAGATGACGGAAAAGATTTACCTGAGGACTATATGAGATCATTGTATGAACGGATATCAAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataattatgtcagacatgatggcttattttctttttggttgttgagttatgcagATGTCTGCTGATGATTTCATAAGAAACAATCGTGGCATTGATGATGGAAAAGATTTGCCAGAGGAATACTTGAGGTCCTTGTTTGAGAGAATATCTAGAA
ttattttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgctcacaatcctatagttctgtaaattgatgtacaaataattatgtcagacatgatggcttattttctttttggttgttgagttatgcagATGTCTGCTGATGATTTCATAAGAAACAATCGTGGCATTGATGATGGAAAAGATTTGCCAGAGGAATACTTGAGGTCCTTGTTTGAGAGAATATCTAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA