Sequence
atgc intronic sequence ATGC exonic sequencegtatggattggagaccttgttgtcttttctaactgtattgtggaatatataattttcagatgaataaatttttactgaatagaattgttttttattttaacctttcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCATTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGATTTGCTGCGGCTGC
Basic information
species | Glycine max |
transcript | GLYMA02G05680.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G05680.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G092776_T04 (Zea mays), 3'ss of exon 6
gtatggattggagaccttgttgtcttttctaactgtattgtggaatatataattttcagatgaataaatttttactgaatagaattgttttttattttaacctttcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCATTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGATTTGCTGC---GGCTGC--------------------------------------------------
||| | || | | | | | | | ||||| |||||||||||||||||||||||||| ||||||| |||||||||| |||| || || ||||| | || || || |||||||||||||| ||||||
--------------------------------------------------------------------------gtgattcatat-gctctaattctcttcgacccgacaggtttagctgcaccagccattgctgcaggatttggtgctctagctccaacactgggcacacttgtccctttcatagGGGCTAGTGGATTTGCTGCTATGGCTGCTGCGGCAGGATCTGTTGCTGGCTCTGTGGCAGTTGCTGCCTCATTTGGAG
upper sequence: GLYMA02G05680.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G092776_T07 (Zea mays), 3'ss of exon 5
gtatggattggagaccttgttgtcttttctaactgtattgtggaatatataattttcagatgaataaatttttactg--aatagaattgttttttattttaacctttcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCATTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGATTTGCTGCGGCTGC
||| ||| || || | | | | |||| || | || ||| || | ||| || | | | | | | || | || | | | | | | ||||| |||||||||||||||||||||||||| ||||||| |||||||||| |||| || || ||||| | || || || |||||||||||||| ||
gta-ggactgcgttccagatcatgtat-ctaa-tgaaatgctgaacatcttggcatcatttggacacactacaccaggtgattcatatgctctaattctcttcgacccgacagGTTTAGCTGCACCAGCCATTGCTGCAGGATTTGGTGCTCTAGCTCCAACACTGGGCACACTTGTCCCTTTCATAGGGGCTAGTGGATTTGCTGCTATGGC
upper sequence: GLYMA02G05680.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 4
gtatggattggagaccttgttgtcttttctaactgtattgtggaatat-ataattttcagatgaataaatttttactgaatagaattgttttttattttaacctttcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCATTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGATTTGCTGCGGCTGC
| | | | || | | ||| | | | | | || |||||| | | || ||| | || || |||| || ||||||||| || ||||| ||||| ||||||||||| || ||||||||||||| ||| | || || | || || || ||||| |||||||| ||||| || |||||
---------gcaaccatagtaggacgtagtaaatatgaaatttctcttcaaaagcttcagacagcatgactgtttttgactt---ttcagttcatttttcactcttcaacagGTTTGGCTGCTCCAGCAATTGCTGCAGGATTTAGTGCATTAGCTCCTACTCTAGGCACAATAATTCCGGTGATTGGAGCAAGTGGGTTTGCAGCAGCTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagatgaataaatttttactgaatagaattgttttttattttaacctttcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCATTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGATTTGCTGCGGCTGC
ttttaac putative branch site (score: 2)
cctttc CT-rich tract
aataaatttttactga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggattggagaccttgttgtcttttctaactgtattgtggaatatataattttcagatgaataaatttttactgaatagaattgttttttattttaacctttcaacagGGTTAGCTGCACCAGCCATTGCTGCAGGTCTTGGTGCATTAGCTCCAACTTTGGGTACTCTGATCCCTGTAATTGGTGCAAGTGGATTTGCTGCGGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC