Sequence
atgc intronic sequence ATGC exonic sequence...atgcaattttcattacttcacatcttatttcgttttatattttccacttctgacattccttttgttctgctttttttttgtttttgtttacctgaaatagCATGTTGAAGATCACCACTTGTATTCGTTGAATTATATGCACTGGGGTGCACCGAAATTGTGGTATGGTGTTGGGGGGAAGGATGCTGTTAAACTCGAGG
Basic information
| species | Arabidopsis thaliana |
| transcript | AT1G08620.2 |
| intron # | 7 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08620.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G156910_T01 (Zea mays), 3'ss of exon 6
-----------atgcaattttcatta-cttcacatcttat-----------ttcgtttta-------tattttccacttctgacattccttttgttctgctttttt--tttgtttttg---tttacctga-aatagCATGTTGAAGATCACCACTTGTATTCGTTGAATTATATGCACTGGGGTGCACCGAAATTGTGGTATGGTGTTGGGGGGAAGGATGCTGTTAAACTCGAGG
|| ||| || ||| |||| | || | || || | |||| | |||| | || | | ||| | || | |||| |||| | | |||| | |||||||||||||||| || ||||| || |||| || ||||| |||||||| || || |||||||||| ||| |||||||||||||| || | ||||
gtaagatgcttttgatattctctttagtttcatagtttgtggttgatgctattgattatggaagctttattatggacttagggtatccatcttgaaatatttcactgatttgaatttgaattgtgcctgttgacagCATGTTGAAGATCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGGAAGGATGCTGTGAATTTGGAGG
upper sequence: AT1G08620.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G31510.1 (Glycine max), 3'ss of exon 5
------atgcaattttcattacttcacatcttatttcgttttatattttccacttctgacattccttttgttctgctttttttttgtttttgtttacctgaaatagCATGTTGAAGATCACCACTTGTATTCGTTGAATTATATGCACTGGGGTGCACCGAAATTGTGGTATGGTGTTGGGGGGAAGGATGCTGTTAAACTCGAGG
| | | | | | | |||| || | | || || | || ||| | ||| | ||| ||| || ||| || || ||||||| ||||||||||| || ||||| |||||||| ||||| ||||| || || ||| ||||||||||||| || || ||||| ||| | || |
gtgtgtgtttacatgtgagagaatgaatccttagttagcatagcatcttt-agttttgataacagctttat---attttctttgtggtttaatta--tggatgcagCATGTGGAAGATCACCATTTATATTCATTGAATTACATGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
upper sequence: AT1G08620.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G36070.1 (Glycine max), 3'ss of exon 4
------atgcaattttcattacttcacatcttatttcgttttatattttccacttctgacattccttttgttctgctttttttttgtttttgtttacctgaaatagCATGTTGAAGATCACCACTTGTATTCGTTGAATTATATGCACTGGGGTGCACCGAAATTGTGGTATGGTGTTGGGGGGAAGGATGCTGTTAAACTCGAGG
| | | | | | | ||||| || | | ||| || | || ||| | ||| | ||| ||| || ||| || || ||||||| |||||||| || || ||||| |||||||| |||| ||||| || || ||| ||||||||||||| || || ||||| ||| | || |
gtgtgtgtttacgtgtgagagaatgaactcttagttggcatagtatcttt-agttttgataacagctttat---attttctttgtggtttaatta--tggatgcagCATGTGGAAGATCATCATTTATATTCATTGAATTACTTGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
upper sequence: AT1G08620.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv14s0036g00570.t01 (Vitis vinifera), 3'ss of exon 8
atgcaattttcattacttc-acatctt-atttcgttttatattttccacttctgacattccttttgttctgctttttttttgtttttgtttacctgaaatagCATGTTGAAGATCACCACTTGTATTCGTTGAATTATATGCACTGGGGTGCACCGAAATTGTGGTATGGTGTTGGGGGGAAGGATGCTGTTAAACTCGAGG
| | || |||| | || || ||| | | | |||| | || | ||| || | |||||| ||| ||| || |||||||||||||||| ||||| ||||||||||| || |||||||||||||| || ||| | ||||||||||| ||| | ||||| ||||| | ||||
-agtatttaatgacacttttagatgttgattatgctgattcttttgtttatttgtttatttgtttatttatttattttttcaaatttattt-ttgagaacagCATGTTGAAGATCATCACTTATATTCGTTGAACTACATGCACTGGGGTGCTCCAAAAATTTGGTATGGTGTCCCAGGGCAAGATGCCCTTAAATTGGAGG
upper sequence: AT1G08620.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S127_125V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------------------atgcaattttcattacttcaca--tcttatttcgttttatatttt-ccacttc----------tgacattccttttgttctgctttttttttgtttttgtttacctgaaatagCATGTTGAAGATCACCACTTGTATTCGTTGAATTATATGCACTGGGGTGCACCGAAATTGTGGTATGGTGTTGGGGGGAAGGATGCTGTTAAACTCGAGG
|| || || || | ||| ||| | |||| | | || ||| ||| || | | | | || || | || | || | | || | ||||||| || || || || || ||||| | ||||||||||| ||||||||||||||| | ||||| |||||| ||| | |||| ||| | ||||
gtaagtaaaaaacctgacctgaattgatttctcgaatgtaacatgcagttatcaaacttgagttgatgtacagactttagtgcgttctgcaacttaccatttcgcgatatggatgttaaccttgtagtcctaatcttcataaattgtggagtatttt--gcagCATGTAGAGGACCATCATTTTTATTCCCTCAATTATATGCATTGGGGTGCACCGAAAATCTGGTACGGTGTTCCTGGGTCTGCAGCTGACAAATTAGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttctgacattccttttgttctgctttttttttgtttttgtttacctgaaatagCATGTTGAAGATCACCACTTGTATTCGTTGAATTATATGCACTGGGGTGCACCGAAATTGTGGTATGGTGTTGGGGGGAAGGATGCTGTTAAACTCGAGG
ttctgac putative branch site (score: 2)
ttccttttgttctgct CT-rich tract
tttttttttgtttttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgcaattttcattacttcacatcttatttcgttttatattttccacttctgacattccttttgttctgctttttttttgtttttgtttacctgaaatagCATGTTGAAGATCACCACTTGTATTCGTTGAATTATATGCACTGGGGTGCACCGAAATTGTGGTATGGTGTTGGGGGGAAGGATGCTGTTAAACTCGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - -tcacatc
- - - - - - - - - - - - - - - - - - - - - -ccacttc
