Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcacatatgattatcacttaacaccttgtcagttgtgtcgtctatgattttgtgtgaacttgaacgagtaattgactgtctgcttcacgcaggttactactatctgtggctttgcgttttattttttaagagattcttgacttcttctactttatgcacatgcagGAACCCCTGAAGTTGGATATTGTTATTAGCTTTCCTGATCATGGATTCCATCTTCGTTTCGATCCGTGGTCTCAG
Basic information
species | Glycine max |
transcript | GLYMA01G37380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G37380.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g49990.3 (Oryza sativa), 3'ss of exon 2
gtttgtcacatatgattatcacttaacaccttgtcagttgtgtcgtctatgattttgtgtgaacttgaacgagtaattgactgtctgcttcacgcaggttactactatctgtggctttgcgttttattttttaagagattcttgacttcttctactttatgcacatgcagGAACCCCTGAAGTTGGATATTGTTATTAGCTTTCCTGATCATGGATTCCATCTTCGTTTCGATCCGTGGTCTCAG
|| ||| | || | | | | || |||| | || | | || | || |||| || || ||| || | ||||| || || ||||||||| |||| || ||||||||||| ||||| ||||| || || |||||||| ||||| |||
------------------------------------------------------------------------gttcgtgatagcgtg--tggctctgtttgctaccaaatgcgccgccag----taaagctcaactgattgtttgctgtcg----tttctgtggcttcagGAGCCTCTAAAGTTGGATTTTGTCATAAGCTTTCCTGACCATGGGTTCCACCTGCGCTTCGATCCTTGGTCACAG
upper sequence: GLYMA01G37380.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G51130.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgtcacatatgattatcacttaacaccttgtcagttgtgtcgtctatgattttgtgtgaacttgaacgagtaattgactgtctgcttcacgcaggttactactatctgtggctttgcgttttattttttaagagattcttgacttcttctactttatgcacatgcagGAACCCCTGAAGTTGGATATTGTTATTAGCTTTCCTGATCATGGATTCCATCTTCGTTTCGATCCGTGGTCTCAG
||| || || | || | || | | | | || |||| | | || ||| || || | ||| | | | || ||||||||| || |||| ||||| |||||||||||||||| |||||||| || |||||||| || ||||| |||||||||
--------------------------------------------------------------gtttgtac---taggtcacggattgtattagata--cttcttttatcca-acttatcttcattgtttgttgagttttctatgattccgttgcct-------catgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCATCTTCGATTTGATCCCTGGTCTCAG
upper sequence: GLYMA01G37380.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g02970.t01 (Vitis vinifera), 3'ss of exon 2
gtttgtcacatatgattatcacttaacaccttgtcagttgtgtcgtctatgattttgtgtgaacttgaacgagtaattgactgtctgcttcacgcaggttactactatctgtggctttgcgttttattttttaagagattcttgacttcttctactttatgcacatgcagGAACCCCTGAAGTTGGATATTGTTATTAGCTTTCCTGATCATGGATTCCATCTTCGTTTCGATCCGTGGTCTCAG
|||| | ||| | ||| | || | ||| ||| || ||| | | | | | || | | || | | ||| | || | | || ||||| || | ||| ||||||| || ||||||||||| |||||||| || ||||||||||| ||||| ||||| |||
--------------------------------------------------------gtgtcatctt--attgttaagtatct-tgcatttccagca--ttgcta--aggggcatatcaggatcttgctact---gaaacatctcactgatatgacaattt----atacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCATCTTCGTTTTGATCCTTGGTCGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgcgttttattttttaagagattcttgacttcttctactttatgcacatgcagGAACCCCTGAAGTTGGATATTGTTATTAGCTTTCCTGATCATGGATTCCATCTTCGTTTCGATCCGTGGTCTCAG
tcttgac putative branch site (score: 3)
ttttattttttaagag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcacatatgattatcacttaacaccttgtcagttgtgtcgtctatgattttgtgtgaacttgaacgagtaattgactgtctgcttcacgcaggttactactatctgtggctttgcgttttattttttaagagattcttgacttcttctactttatgcacatgcagGAACCCCTGAAGTTGGATATTGTTATTAGCTTTCCTGATCATGGATTCCATCTTCGTTTCGATCCGTGGTCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA