Sequence
atgc intronic sequence ATGC exonic sequence...tcctataatgcattgttctttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcagAAGGGTCGTTGCCTCTTCCTTGGTCTATTAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTACTTTTCTCCATGAAGAAGCTCAGAGGCCTGTAAT
Basic information
| species | Glycine max |
| transcript | GLYMA09G37580.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 3
tcctataatgcattgttctttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatg---aattgtgcagA--AGGGTCGTTGCCTCTTCCTTGGTCTATTAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTACTTTTCTCCATGAAGAAGCTCAGAGGCCTGTAAT---
||| || || || | | | | | | | || | | | | | | || |||| || | || |||||| | |||||| || ||||| || ||| | || ||||||| ||| |||||||||||||| || || ||| ||||||| |||||||||||| | ||||| || ||
------gttgcgttaaatttg--gcccaactgtttcatttcagtataactctattctgaagtgtcttgtatttatctgatatttgtcttggataattgtattaaacagGGTCTTTACCTCTCCCATGGGCCATCAGAATGAGAATAGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTA
upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------------------------------------tcctataatgcat-tgttctttctgctta--gcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcagAAGGGTCGTTGCCTCTTCCTTGGTCTATTAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTACTTTTCTCCATGAAGAAGCTCAGAGGCCTGTAAT---
| || | | || | | || | | ||| | || | ||| | | ||| | |||| | | || | |||| | | | ||||| | ||||| |||||||| || |||||||| |||| ||||| || ||||| |||||| |||| || ||||||||||| | || || || ||
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatctta-tatgatttatgattcacctata-gGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
tcctataatgcattgttctt--tctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcagAAGGGTCGTTGCCTCTTCCTTGGTCTATTAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTACTTTTCTCCATGAAGAAGCTCAGAGGCCTGTAAT---
| || ||| || | || || | || | ||| | || | | | ||| ||| ||||| | | | | || ||| |||||||| || ||| | ||||||||||||||||| ||||||||||| ||||| || ||||||| |||||||||||| | || || |||||
----aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacat-cttgaaccttcacatacccatctaataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G01300.1 (Arabidopsis thaliana), 3'ss of exon 3
----tcctataatgcattgttctttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcagAAGGGTCGTTGCCTCTTCCTTGGTCTATTAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTACTTTTCTCCATGAAGAAGCTCAGAGGCCTGTAAT---
| | || || || |||| || | || |||| | || | || || | || | || ||| || | || | ||| |||||||| ||||||||||| ||||| ||| | ||||| |||||| | ||||||||||| ||||| | ||| || || ||||||||| | ||| || ||
tgtgtttaaaaagacacagtgcttt-tgtatgat----ttatcttctcagttatcattgat--gcaaatctttttatttgtgaattaacttgtgcttcgtgttgaagGGTCCTTGCCTCTTCCATGGTCAATTCGGATGAAGATTGCATTAGGTGCTGCAAAGGGTCTCAGTTTCCTTCACGAAGAAGCTTTAAAGCCGGTCATTTA
upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 3
tcctataatgcattgttctttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcagAAGGGTCGTTGCCTCTTCCTTGGTCTATTAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTACTTTTCTCCATGAAGAAGCTCAGAGGCCTGTAAT---
| || || | | | ||| || || || | ||| || | || | || || || | ||| | ||||||| |||||||||||||||||||| | ||||| |||||| | ||||||||||||||||| | ||| ||||||||||||||| || |||||| ||
-------------------gtatgtataaatcaaaccattttaaagttgtt-tccatgtttaa-tcgtttttcttatgatactggtgctttcatgttta-aagGGTCCTTGCCTCTTCCTTGGTCTATCCGGATGAAGATTGCATTAGGTGCTGCAAAAGGTCTCAGTTTCCTCCATGAAGAAGCTTTGAAGCCTGTTATATA
upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 2
tcctataatgcattgttc-tttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcagAAGGGTCGTTGCCTCTTCCTTGGTCTATTAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTACTTTTCTCCATGAAGAAGCTCAGAGGCCTGTAAT---
||| | || | ||||| | | | |||| | ||| ||| | | | ||| | | | | | | ||| | | || | || ||||| ||||||||| || |||||||||||||||||||||| || |||||||| | ||||| || ||||||||| ||| ||| || ||
--gtatg-tctatcgcaaacctctgcacatc-ttcttctttctgagggctttgag-gtgtctcgtctaattaccatgttttt-cttttttcatttgggttcagGGACC-TTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAGCTAAAGGTCTCGCCTTTCTTCACGAAGAAGCTGAGAAGCCAGTCATATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcagAAGGGTCGTTGCCTCTTCCTTGGTCTATTAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTACTTTTCTCCATGAAGAAGCTCAGAGGCCTGTAAT
tggtaac putative branch site (score: 2)
attgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcctataatgcattgttctttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcagAAGGGTCGTTGCCTCTTCCTTGGTCTATTAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTACTTTTCTCCATGAAGAAGCTCAGAGGCCTGTAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - aatgcat
- - - - - - - - - -ttctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaccat
