Sequence
atgc intronic sequence ATGC exonic sequence...cttctttcagaagacatactcatctctgcacattttaatcttgtttaactccatactaagttctttctatgtttcctgtttggttttaatgcttatacagGACTTCTTTGAGGATGTAGGACCACTGCTTAGCATGCAGTTGGGAGGCCAAGCTCTCGAAGGATTGTTTCAAGTATTTAACTCCTATGTGAACATGCTCA
Basic information
species | Glycine max |
transcript | GLYMA08G23840.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G23840.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G49830.3 (Arabidopsis thaliana), 3'ss of exon 4
-cttctttcagaagacatactcatctctgcacattttaatcttgtttaactccatactaagttctttctatgtttcctgtttggttttaatgctta--tacagGACTTCTTTGAGGATGTAGGACCACTGCTTAGCATGCAGTTGGGAGGCCAAGCTCTCGAAGGATTGTTTCAAGTATTTAACTCCTATGTGAACATGCTCA
||| | || | | | | | || | | | | |||| | | || | | |||| |||| | | | || | ||||||||||||||||| |||||||| ||||| || ||||| |||||| | ||||||| ||||| |||||| || |||||||| ||||| | ||||
tcttagctgctctgataggcagaggatt-cccaagtggactgtcatgaactttgga-tgtatttgtcaagtagatcct-tttgataatggtattttgttgcagGACTTCTTTGAGGACGTAGGACCTCTGCTAAGTATGCAATTGGGAAGTAAAGCTCTGGAAGGTCTGTTTCGGGTGTTTAACTCATATGTAGATGTGCTGG
upper sequence: GLYMA08G23840.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0018g01920.t01 (Vitis vinifera), 3'ss of exon 3
-cttctttcagaagacatactcatctctgcacattttaatcttgtttaactccatactaagttctttct-atgtttcct--gtttggtttt---aatgcttatacagGACTTCTTTGAGGATGTAGGACCACTGCTTAGCATGCAGTTGGGAGGCCAAGCTCTCGAAGGATTGTTTCAAGTATTTAACTCCTATGTGAACATGCTCA
|| || | | || | ||| |||| | ||||| || | || | | || || || ||| ||| | | | |||| | || | | ||||| ||||||||||||||||||||||| | ||||||||||| ||||| ||| | || ||||| ||||| || || ||||| || |||||||| ||||||
gtttattctccatggaatg-tggtcta-----atttgattcttggttc-cataatggtgactttttccttatggttcttttgctgcattttccaattgttcttgcagGATTTCTTTGAGGATGTAGGACCACTCTTAAGCATGCAGTTAGGAGGTCAAACACTTGAAGGCTTGTTCCAGGTGTTTAATTCATATGTGAATTTGCTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taactccatactaagttctttctatgtttcctgtttggttttaatgcttatacagGACTTCTTTGAGGATGTAGGACCACTGCTTAGCATGCAGTTGGGAGGCCAAGCTCTCGAAGGATTGTTTCAAGTATTTAACTCCTATGTGAACATGCTCA
ttttaat putative branch site (score: 3)
ttttaatgcttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttctttcagaagacatactcatctctgcacattttaatcttgtttaactccatactaagttctttctatgtttcctgtttggttttaatgcttatacagGACTTCTTTGAGGATGTAGGACCACTGCTTAGCATGCAGTTGGGAGGCCAAGCTCTCGAAGGATTGTTTCAAGTATTTAACTCCTATGTGAACATGCTCA
- - - - - - - catactc
- - - - - - - - - - - -ctctgca
- - - - - - - - - - - - - - - - - - - - - - - - - ccatact