Sequence
atgc intronic sequence ATGC exonic sequencegtttgtacttttaaaccctgcataattataccatctcccttatgcgtacatgctgcactgagaaagtgtattagaatttagaaatggtcctaaattatgtattacattcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATCGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
Basic information
species | Glycine max |
transcript | GLYMA04G42390.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G42390.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G032337_T02 (Zea mays), 3'ss of exon 7
gtttgtacttttaaaccctgcataattataccatctcccttatgcgtacatgctgcactgagaaagtgtattagaatttagaaatggtcctaaattatgtattacattcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATCGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
|| || | |||| | || || | | || ||| || || ||| | || || || | || | |||| |||||||||||||||||||||||| | ||||| || | || |||||||| ||||| |||||||| || || || ||||| | || || || ||
---------gtttgtttcttaacaattgttttattgtttttccgtctgt-tgtagcattgg------------------agcaattgctttac----tgacatagagatatcttggcagATACTTGGCTCCTGAATACTTCATGCATGGCAAGGTGGGCAACAAAATCGATGTGTATGCTTTCGGTGTTGTACTTCTGGAGCTCATCTCTGGCAGGAAA
upper sequence: GLYMA04G42390.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
gtttgtacttttaaaccctgcataattataccatctcccttatgcgtacatgctgcactgagaaagtgtattagaatttagaaatggtcctaaattatgtattacattcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATCGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
| || | ||| ||| || || ||| ||| | || |||||| || ||||| || | || | || || ||| ||||| ||||||||||| || ||||||||||| || || || ||||||||||| ||||| ||||||||||| || || ||||| ||| | ||||| || |||||
-------------------gtatgaa-gtac--tctaggttttgggta-atgtttcat---gaaagttc--------ttgaaaatgttcttgtgcta-atcttctgtt--tttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
upper sequence: GLYMA04G42390.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0001g01680.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------------------gtttgtacttttaaaccctgcataattataccatctcccttatgcgtacatgctgcactgagaaagtgtattagaat-ttagaaatggtcctaaattatgt--attacattcattta---tgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATCGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
| ||| | | | | | | | | || ||| | | || | | | || | | || ||| | | ||| | | | || | ||||| |||| ||||||||| |||||||||||||||||||||| |||||||||||||| ||||| |||||||| ||||| ||||| || ||||||||||||||||| || |||||
gtttgtgcttcttctctagtagctataacttctatgtcccacattcttgtcatttttcagaagatcaataaaccccactattttgaattatggctttaaaatcttgagtaaaaaagttattacttgtcattgagaaagttcagaacatttattttctctgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGAGAAGATAGATGTCTACGCATTTGGTGTTGTCCTCCTTGAGCTTCTTTCGGGAAGAAAA
upper sequence: GLYMA04G42390.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S242_29V6.1 (Physcomitrella patens), 3'ss of exon 8
gtttgtacttttaaaccctgcataattataccatctcccttatgcgtacatgctgcactgagaaagt-gtattagaatttagaaatggtcctaaattatgtattacattcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATCGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
|| |||| || | | ||| | | ||| | | || | | | || | || | || | | || || | | ||| |||||||| || |||||||||||||| || | || || || ||||||||||| || ||||||||||| ||||| | |||||| | | || || ||
---------------gggtgtgggattaaactgtggcgctttcctgcagccactgtatcatcgacgtagcagtcgatcgttgatacataactgactggcgttatatctctac-----cagGTACTTGGCCCCGGAATACTTCATGTATGGGAGGGTGAACGACAAGATCGATGTGTACGCATTCGGTGTAGTGCTTTTAGAGCTTATCACGGGTAGGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgtattagaatttagaaatggtcctaaattatgtattacattcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATCGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
tcctaaa putative branch site (score: 2)
ttcattt putative PPT
taaattatgtattaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtacttttaaaccctgcataattataccatctcccttatgcgtacatgctgcactgagaaagtgtattagaatttagaaatggtcctaaattatgtattacattcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATCGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA