Sequence
atgc intronic sequence ATGC exonic sequencegtaaataatttttttgttacttcaaatagatatctgattatgtcatatctactaaagatttgattaattaactattatctgaacctttcttgtgatgattgtaatgttgcagCAGAGACTAGTTAGAGATTTTTACAATATCCTTAACGAAGTAAAGACTAGGGAAATTCCATCTGCTCTAGAGCTTCCGGATTCATTTGATCAACTGGTTT
Basic information
species | Glycine max |
transcript | GLYMA19G03460.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G03460.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G01040.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaataatttttttgttacttcaaatagatatctga-ttatgtcatatctactaaagatttgattaattaactattatctgaacctttcttgtgatgat-tgtaatgttgcagCAGAGACTAGTTAGAGATTTTTACAATATCCTTAACGAAGTAAAGACTAGGGAAATTCCATCTGCTCTAGAGCTTCCGGATTCATTTGATCAACTGGTTT
|| | | ||| || || | || | | ||| ||||| ||||| | | || | | | || | | | | || | | | || |||||||||||||||||||||||||||||||||| || || || ||||||| ||| ||||||||| || | || ||||||| || || ||| |||||||||||
gtgagtgattgcttcttttc-------aggtgtttgaattatg----atctaaaactctctgtatcagtatgtttaagtccggatttcttttcttttcacacgttctgttgcagCAGAGACTAGTTAGAGATTTTTACAAAATTCTAAATGAAGTAAGCACTCAAGAAATTCCAGATGGTTTAAAGCTTCCAGAGTCTTTTAGTCAACTGGTTT
upper sequence: GLYMA19G03460.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G01040.2 (Arabidopsis thaliana), 3'ss of exon 2
gtaaataatttttttgttacttcaaatagatatctga-ttatgtcatatctactaaagatttgattaattaactattatctgaacctttcttgtgatgat-tgtaatgttgcagCAGAGACTAGTTAGAGATTTTTACAATATCCTTAACGAAGTAAAGACTAGGGAAATTCCATCTGCTCTAGAGCTTCCGGATTCATTTGATCAACTGGTTT---
|| | | ||| || || | || | | ||| ||||| ||||| | | || | | | || | | | | || | | | || |||||||||||||||||||||||||||||||||| || || || ||||||| ||| ||||||||| || | || ||||||| || || ||| |||||||||||
gtgagtgattgcttcttttc-------aggtgtttgaattatg----atctaaaactctctgtatcagtatgtttaagtccggatttcttttcttttcacacgttctgttgcagcagAGACTAGTTAGAGATTTTTACAAAATTCTAAATGAAGTAAGCACTCAAGAAATTCCAGATGGTTTAAAGCTTCCAGAGTCTTTTAGTCAACTGGTTTCGG
upper sequence: GLYMA19G03460.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0108g01520.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------gtaaataatttttttgttacttcaaatagatatctgatta-----tgtcatatctactaaagatttgattaattaactattatctgaacctttcttgtgatgattgtaatgttgcagCAGAGACTAGTTAGAGATTTTTACAATATCCTTAACGAAGTAAAGACTAGGGAAATTCCATCTGCTCTAGAGCTTCCGGATTCATTTGATCAACTGGTTT
||| || | ||||| | | ||| | |||||| | | | | | | | || | ||| | | |||| | | || | | | ||| | | || |||||||||| |||||||||||||||||||| ||||| || |||| || ||| |||| | ||| || |||| ||||||| ||| |||| |||||| ||||
gtaaattttgtctttttcttatcctgtagatgttatttttag-attgataatgcccgtttgattagttttttttttctttggtggaaatattatttgt--gttgttatttaagccaat-tcctcatggtgatggtgctgcagCAGAGGCTAGTTAGAGATTTTTACAAGATCCTCAATCAAGTGAACACTGAGGAACTCCCAGATGGTCTAAAGCTTCCAGATACATTCAGTCAACTTGTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgattaattaactattatctgaacctttcttgtgatgattgtaatgttgcagCAGAGACTAGTTAGAGATTTTTACAATATCCTTAACGAAGTAAAGACTAGGGAAATTCCATCTGCTCTAGAGCTTCCGGATTCATTTGATCAACTGGTTT
aattaac putative branch site (score: 2)
attaattaactattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaataatttttttgttacttcaaatagatatctgattatgtcatatctactaaagatttgattaattaactattatctgaacctttcttgtgatgattgtaatgttgcagCAGAGACTAGTTAGAGATTTTTACAATATCCTTAACGAAGTAAAGACTAGGGAAATTCCATCTGCTCTAGAGCTTCCGGATTCATTTGATCAACTGGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT