Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatgatattttattggtctaagatactccaagtcaattagttcacccggactatctcttgactgaatagttttttatgctgtagAGATATTTGGGTACGGTCAGAGAAGAGGACACCCTAAATATTCTCCTGGAGTTTGTTCCTGGTGGATCCATATCATCACTATTGGGGAAGTTTGGGGCTT
Basic information
species | Glycine max |
transcript | GLYMA19G42340.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G09000.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagta-----tgatattttattggtctaagatactccaagtcaattagttcacccggactatctct-tgactgaatagttttttat------gctgtagAGATATTTGGGTACGGTCAGAGAAGAGGACACCCTAAATATTCTCCTGGAGTTTGTTCCTGGTGGATCCATATCATCACTATTGGGGAAGTTTGGGGCTT
|| |||| || |||| | | ||| | | | | | | ||| | | ||||| | | ||| | |||||||| || ||||||||||||||||| || || ||||| || ||||| ||||| || || ||||||||||| |||||||| |||||||| || |||| ||| ||||| |||
gtaagtaactgttggtattgtctccttctcaatgcatacggattcaacacttc-cttgtgttatctatctaactcaggtattttttattttctggccttagAGATATTTGGGTACAGTGAGGGAAGATGATACCCTGAATATCCTTCTCGAGTTTGTTCCCGGTGGATCGATATCATCGCTCTTGGAGAAATTTGGACCTT
upper sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 3
----gtgagtatgatattttattggtctaagatactccaagtcaattagttcacccggactatctcttgact---gaatagttttttatgctgtagAGATATTTGGGTACGGTCAGAGAAGAGGACACCCTAAATATTCTCCTGGAGTTTGTTCCTGGTGGATCCATATCATCACTATTGGGGAAGTTTGGGGCTT
| | | | |||| | ||| | || | ||| | ||| || | | | ||| | || ||| || || |||||||||||||||||||| || ||||| || || | ||||| | || || ||||||||||||||||| ||||| ||||| |||| ||| ||||| || |
gtaagcaataacgttattgttttgttgcaatgctgattgattcagtgtgtttgtgttttcttttttataacttttgcattctttgtttggccttagAGATATTTGGGTACGGTGAGGGAAGATGAAACTTTGAATATCTTGCTTGAATTTGTTCCTGGTGGATCTATATCTTCACTCTTGGAGAAATTTGGAGCCT
upper sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------------gtgagtatgatattt-tattggtctaagatactccaagtcaatta-gttcacccggactatctcttgactgaatagttttttatgctgtagAGATATTTGGGTACGGTCAGAGAAGAGGACACCCTAAATATTCTCCTGGAGTTTGTTCCTGGTGGATCCATATCATCACTATTGGGGAAGTTTGGGGCTT
|||||| | || || | | | || | || | || | | | || | | | | | |||| | || |||| |||||||||| ||||| || ||||| ||| | |||||| | |||| |||||||||||||||||||| |||||||| |||||||| ||||| |||
gtgagtatgatcttctacctttttcttattctgatattttccagacaaaatgaatgaaattgagtagaaaatgggtaataatgtttgacaaagtaaactgactatacttatcagggttccaattacattcgttg--ttttcgttatgcagAGGTATTTGGGTATAGTCAGGGAGGAGGAGACCTTGAATATTTTGTTGGAATTTGTTCCTGGTGGATCCATCTCATCACTTTTGGGGAAATTTGGATCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtcaattagttcacccggactatctcttgactgaatagttttttatgctgtagAGATATTTGGGTACGGTCAGAGAAGAGGACACCCTAAATATTCTCCTGGAGTTTGTTCCTGGTGGATCCATATCATCACTATTGGGGAAGTTTGGGGCTT
tcttgac putative branch site (score: 3)
ttttttat putative PPT
tgaatagttttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatgatattttattggtctaagatactccaagtcaattagttcacccggactatctcttgactgaatagttttttatgctgtagAGATATTTGGGTACGGTCAGAGAAGAGGACACCCTAAATATTCTCCTGGAGTTTGTTCCTGGTGGATCCATATCATCACTATTGGGGAAGTTTGGGGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA