Sequence
atgc intronic sequence ATGC exonic sequencegtaaatccatgaatcctatatcttttgcttcaatttcttgcataacttctcacattattagaggatctatatatacttattctggttgtctcacagAACGTTGTGGGTAAATGGAGCTCAAAGCTATTTGCAATTGCGTTGCTTGCTTCCGGTCAGAGTTCAACCATAACCGGAACATATGCTGGACAATACGTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G15960.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G15960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G069198_T03 (Zea mays), 3'ss of exon 10
--gtaaatccatgaatcct-atatcttttgcttcaatttcttgcataacttctcacat-tattagaggatctatatatacttattctggttgtctcacagAACGTTGTGGGTAAATGGAGCTCAAAGCTATTTGCAATTGCGTTGCTTGCTTCCGGTCAGAGTTCAACCATAACCGGAACATATGCTGGACAATACGTTA
| | | | | | | | || |||| | || | | ||| || | |||| | | | | || | | | ||| |||| || | || || |||||||||||| | |||||| |||| ||| | || || ||||||||||| || || || || ||||||||||||||||| || |
gagcttctgcttcagttttgaaatgttttttgtgaagtctatatatacttttcggtaaatattcaaatctgacactgcattttctttactgttcttttagAATGTCCTTGGAAACTGGAGCTCAAAGTTGTTTGCAGTTGCTTTGTTGGCATCTGGTCAGAGTTCTACAATTACGGGGACATATGCTGGACAATATGTCA
upper sequence: AT1G15960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G02680.1 (Glycine max), 3'ss of exon 8
---------------------------------------gtaaatccatgaatcctatatcttttgcttcaatttcttgcataacttctcacattattagaggatctatatatacttattctggttgtctcacagAACGTTGTGGGTAAATGGAGCTCAAAGCTATTTGCAATTGCGTTGCTTGCTTCCGGTCAGAGTTCAACCATAACCGGAACATATGCTGGACAATACGTTA
|| | | | || | | | | ||| ||| || | | || | | ||| | ||||| || | ||||||| || |||| |||||||||||||| |||||||||||||| || ||||| || ||||| ||||| |||||||| ||||||||||| ||||||||||| |
gtacgtgacactgccacatgtcttcttatgacaaacaccatatgtgcctagttcttgaacatcatatatcatttttgctggaaagtgtgctaataaaatcattgatgataatttcttatatgggcca-cacacagAATGTCTTGGGCAAATGGAGCTCAAAACTATTTGCAATTGCTTTACTTGCCTCAGGTCAAAGTTCTACCATAACAGGAACATATGCAGGACAATACGTCA
upper sequence: AT1G15960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G23320.1 (Glycine max), 3'ss of exon 10
--------------------------------gtaaat-ccatgaatcctatatcttttgcttcaatttcttgcataacttctcacattattagaggatctatatatacttattct--ggttgtctcacagAACGTTGTGGGTAAATGGAGCTCAAAGCTATTTGCAATTGCGTTGCTTGCTTCCGGTCAGAGTTCAACCATAACCGGAACATATGCTGGACAATACGTTA
||| |||| | | | || ||| || |||| | | | | |||| | || || | || || | || | ||||||| || |||| |||||||| ||||| |||||||||||||| || ||||| || ||||| ||||| || ||||| ||||||||||| || ||||| || |
gtatgtgactctaccatatgtgttcttatgtgacaaacaccatatgtacctagttcttcacttatcctttttgc-tggaaagtgtcttcattaaaccattgatgataatttcttatatggaccacacacagAATGTCTTGGGCAAATGGAGTTCAAAACTATTTGCAATTGCTTTACTTGCCTCAGGTCAAAGTTCTACTATAACAGGAACATATGCAGGGCAATATGTCA
upper sequence: AT1G15960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G00590.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------------gtaaatccatgaatcctatatcttttgcttcaatttct----tgcata-acttctcacattattagaggatctata----tatacttattctggttgtctca---------cagAACGTTGTGGGTAAATGGAGCTCAAAGCTATTTGCAATTGCGTTGCTTGCTTCCGGTCAGAGTTCAACCATAACCGGAACATATGCTGGACAATACGTTA
| | | ||| || | | ||| | |||| | | |||| || | | || || | ||| ||| | | | || | | ||||| || |||| |||||||||||||| ||||||| |||||| |||||||| || ||||| ||||| || || || ||||| || || ||||| || || |
gtatgtgaaaaccggagatgtctttcttaccttgggtatattgtagtagtgctaagtttagttgctgattctttcacaatttaccccaatccttaagcttcatatacatttgttgttggtaaggtgctcataaaatcatagctgatatatctgacatataacatactcagAATGTCTTGGGGAAATGGAGCTCAAAACTATTTGGAATTGCTTTGCTTGCATCGGGTCAAAGTTCTACTATTACAGGAACCTACGCAGGACAGTATGTCA
upper sequence: AT1G15960.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0070g00210.t01 (Vitis vinifera), 3'ss of exon 10
--------------------------------------------------------------------------------------------gtaaatccatgaatccta-tatc-ttttgcttcaatttcttg-cataacttctcacattattagaggatctatatatacttattctggttgtctcacagAACGTTGTGGGTAAATGGAGCTCAAAGCTATTTGCAATTGCGTTGCTTGCTTCCGGTCAGAGTTCAACCATAACCGGAACATATGCTGGACAATACGTTA
| || || || || | ||| |||||| | |||| | |||| || ||| || | ||| | | | | || || | || ||||| || | || ||||||||||||||||| ||||| ||||| ||||| || || ||||||||||| || || || ||||||||||| || ||||| || |
gtatgtctctgtagttgtagcaacatgggcatttattgttatcatccttcaatctctcatttagcttctaaccagattgtgctaaaatccatttcaaatcaggattcttggtatggttttgccttttcttctgaacccaactgtccagatt-tttcatgatat-tgttaatttgttatcatt----tgcagAATGTATTAGGCAAATGGAGCTCAAAGCTTTTTGCTATTGCTTTGCTAGCATCTGGTCAGAGTTCTACGATCACGGGAACATATGCAGGGCAATATGTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataacttctcacattattagaggatctatatatacttattctggttgtctcacagAACGTTGTGGGTAAATGGAGCTCAAAGCTATTTGCAATTGCGTTGCTTGCTTCCGGTCAGAGTTCAACCATAACCGGAACATATGCTGGACAATACGTTA
ttctcac putative branch site (score: 2)
ttgtctc putative PPT
atctatatatacttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatccatgaatcctatatcttttgcttcaatttcttgcataacttctcacattattagaggatctatatatacttattctggttgtctcacagAACGTTGTGGGTAAATGGAGCTCAAAGCTATTTGCAATTGCGTTGCTTGCTTCCGGTCAGAGTTCAACCATAACCGGAACATATGCTGGACAATACGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA