Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatcaattcacttttattttggttcagcttcagatgatgttccattgaccttaaataacttgtttttgtaatgatattaaatatgtgaagGTGCGGGCATCAGCAATTATCACAAATGCACCGTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
Basic information
species | Glycine max |
transcript | GLYMA05G32100.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G32100.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G64740.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------gtaagtatcaattcacttttattttggttcagcttcagatgatgttccattgaccttaaataacttgtttttgtaatgatattaaatatgtgaagGTGCGGGCATCAGCAATTATCACAAATGCACCGTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
| | | || ||| | | | || | | | || | || | | ||| | | | | | ||||| | || | || | || | ||||||| || || ||||||||||| ||||||||||||||||| ||||||||||| || ||||||||||| |||||||
gtaaatgatatactttttaaagctctaaaccttcttctttgtaaattacgtcttgccatttattgaaatggttcctgactcttgatttcatctacaaaactt--ttgttgaagATACGAGTCTCTGGGGTTCTATCAAATGCTCCTTACCTTCTGAATGTCGATTGTGATCACTACATCAACAATAGCAAAGCTCTTAGAGAAGCAATGTGTT
upper sequence: GLYMA05G32100.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G39350.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagtatcaattcacttttattttggttcagcttcagatgatgttccattgaccttaaataacttgtttttgtaatgatattaaatatgtgaagGTGCGGGCATCAGCAATTATCACAAATGCACCGTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
|||||||| ||| || | | || | | || | | || |||| | |||| | | || || | | | ||||| | || | || || || | |||| || || || ||||| ||||| ||||||||||||||||| ||||| ||||| ||| |||||||| |||||||||
gtaagtat-aatgtgtttctttatttatgaatctctcttttcggagcc-ctgacttctcataaactaaaactc--atcttacttcttct-tgaagATCCGAGTCTCTGCTGTTCTATCAAACGCTCCTTACCTTCTTAATGTCGATTGTGATCACTACATCAACAACAGCAAAGCAATTAGAGAATCTATGTGTT
upper sequence: GLYMA05G32100.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G09870.1 (Arabidopsis thaliana), 3'ss of exon 8
----gtaagtat---caattcacttttat----tttggttcagcttcagatgatgttccattgaccttaaataacttgtttttgtaatgatattaaatatg--tgaagGTGCGGGCATCAGCAATTATCACAAATGCACCGTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
||| ||| ||| || | | | |||| | || | | || | | | || | | ||| || || | ||| || |||| ||||| | || | || | | || | ||||||| || |||||||| ||||| ||||||||||||||||| || |||||||| || ||||||||||| |||||||
gtaaataattatgctcaactctccagtgtattctttgaattgatttatgtttatctctcgctaacttcc--tgactctttcttctcatgttaccgtatataattgaagATACGAGTCTCTGGAGTTCTATCAAATGCTCCTTATCTTCTAAATGTCGATTGTGATCACTACATCAATAATAGCAAAGCTCTTAGAGAAGCAATGTGTT
upper sequence: GLYMA05G32100.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G21770.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagtatcaattcacttttattttggttcagcttcagatgatgttccattgaccttaaataacttgtttttgtaatgatattaaatatgtgaagGTGCGGGCATCAGCAATTATCACAAATGCACCGTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
|| || ||| ||| ||| ||||| | ||| |||| | ||| | | | |||| | ||| | ||||| | |||| ||| || || || ||||||| || || ||||| ||||| || |||||||| ||||| ||||| ||||||||| ||||||||||||||||||
gttaggatctgttccttttcatttttctct--cttt---tgatttccca--aatttcgtaaaactaaactcattaacctctct-------tgaagATCCGGGTATCTGCTGTTCTCTCAAATGCTCCTTACCTTCTTAATGTGGACTGTGATCATTACATCAACAACAGCAAGGCAATTAGAGAAGCTATGTGTT
upper sequence: GLYMA05G32100.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0031g02060.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------------------------------gtaagtatcaattc--acttttattttggttc--agcttcagatgatgttccattgaccttaaataacttg--tttttgtaatgatattaaatatgtg-aagGTGCGGGCATCAGCAATTATCACAAATGCACCGTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
| || || ||||||| | | | | | ||| || | ||| | ||| ||| ||| | || | ||| || | |||||||| | |||||| | || ||||||| |||||||||||||| ||||| ||||| || || || ||||||||||||||||||||||||||||||||||
gtaaaccttaaatcaataacaccttcatagatcctttttctttggttgcctttccttgtcttctgtttttacttttagtataatacctggtttcgatgaataaacacttggcacagaatttattgagctttgttgctgtttttatgaatatccaagGTGCGAGTTTCAGCAGTCATTTCAAATGCCCCGTATCTTCTGAACGTTGACTGTGACCATTATATCAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgttccattgaccttaaataacttgtttttgtaatgatattaaatatgtgaagGTGCGGGCATCAGCAATTATCACAAATGCACCGTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
aaataac putative branch site (score: 2)
ttaaataacttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatcaattcacttttattttggttcagcttcagatgatgttccattgaccttaaataacttgtttttgtaatgatattaaatatgtgaagGTGCGGGCATCAGCAATTATCACAAATGCACCGTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC