Sequence
atgc intronic sequence ATGC exonic sequencegtagaaaacattacaaagtttttcaacttctgaaaactagaaaagttcttgtgatctcattcttgctgataatcacacgcagATCGGGTGGATTTATGGATCGGTGACTGAAGATATCCTGACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTGTACTGTATGCCTAAGCGTGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39350.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39350.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM5G840940_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------gtagaaaacattacaaa--gtttttcaacttctgaaa--actagaaaagtt----cttgtgatctca------ttcttgct-----gataatcacacgcagATCGGGTGGATTTATGGATCGGTGACTGAAGATATCCTGACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTGTACTGTATGCCTAAGCGTGCAG
| | | | |||| || ||| | ||||| | | ||||| | | | ||| | || | ||| ||| | | | || | || |||||||||||||| || ||||| |||||||| ||||| ||||||||||| |||||||| ||| ||||||||||||| ||||| ||| | |||
gtaactttggcccatcatgtctttgtttttccttctcccatgtagtttccagatcaggctcttcaaactgtgtttgtgcccttgaaataaattgaaaaactgcaacctagcatccaagaatacttttagctaactcgatgaaaatatctagGTTGGTTGGATTTATGGATCTGTCACTGAGGATATCCTCACGGGCTTCAAGATGCACTGCCATGGTTGGCGATCTGTGTACTGCATGCCCAAGAGACCAG
upper sequence: AT4G39350.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G15380.1 (Glycine max), 3'ss of exon 12
---------gtagaaaaca-ttacaaagtttttcaacttctgaaaactagaaaa---gttcttgtgatctcattcttgctgataatcacacg---------cagATCGGGTGGATTTATGGATCGGTGACTGAAGATATCCTGACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTGTACTGTATGCCTAAGCGTGCAG
||||||| | || ||| | || |||| ||| ||||| | | ||||||| |||| | | ||| | |||||||| ||||| || ||||| || |||||| |||| || || || |||||||||||||| ||| | |||||||| || || |||||||| | |
gtaagtatcatagaaaaaaattgttttgttaattctttttgaaaaattagtcttctcattcttatatttattctcttgctcataaaccgttggcgttttaccagGTTGGGTGGATATATGGTTCTGTGACAGAGGATATCTTGACTGGATTTAAAATGCATTGCCATGGTTGGCGGTCTGTGTATTGCATTCCTAAGCGGCCTG
upper sequence: AT4G39350.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA05G32100.1 (Glycine max), 3'ss of exon 12
gtagaaaacattacaaa------gtttttcaacttct-----gaaaactagaaa---agttcttgtgatctcattcttgctgataatcacacgc--------agATCGGGTGGATTTATGGATCGGTGACTGAAGATATCCTGACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTGTACTGTATGCCTAAGCGTGCAG
||| | ||| || ||||| || |||| |||| ||| ||||| | | ||||||| |||||| || || | |||||||| ||||| || ||||| || |||||| |||| || || || |||||||||||||| ||| | |||||||| || || |||||||| | |
gtaagtatcatagaaagaaatttgttttgtaaattctttttgaaaaattagtcttctcattcttatatttcttctcttgctcataatcgttggcttgctaccagGTTGGGTGGATATATGGTTCTGTGACAGAGGATATCTTGACTGGATTTAAAATGCATTGCCATGGTTGGCGGTCTGTGTATTGCATTCCTAAGCGGCCTG
upper sequence: AT4G39350.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv07s0031g02060.t01 (Vitis vinifera), 3'ss of exon 12
----gtagaaaacattacaaagtttttcaa--cttctgaaaactagaaaagttcttgtgatctcattcttgct--gataatcacacgc------agATCGGGTGGATTTATGGATCGGTGACTGAAGATATCCTGACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTGTACTGTATGCCTAAGCGTGCAG
| |||||| | | ||||||| | || |||| | | || || | | |||||| | || ||| || | || | || ||||| ||||| || ||||| || ||||| || || || ||||||||||| |||||||||||| | ||||| ||||| || || ||||| | |
gtaaggagaaaaaaattcaaagttctgaaaaccttccattagcaagttctaccattatcacttcattcctttctaaattttcaaacactgaaccagGTTGGCTGGATATATGGCTCTGTGACAGAGGATATACTAACAGGGTTCAAGATGCACTGCCATGGATGGCGGTCTGTTTACTGCATACCCAAGCGGCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgaaaactagaaaagttcttgtgatctcattcttgctgataatcacacgcagATCGGGTGGATTTATGGATCGGTGACTGAAGATATCCTGACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTGTACTGTATGCCTAAGCGTGCAG
tgctgat putative branch site (score: 3)
aaaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagaaaacattacaaagtttttcaacttctgaaaactagaaaagttcttgtgatctcattcttgctgataatcacacgcagATCGGGTGGATTTATGGATCGGTGACTGAAGATATCCTGACGGGTTTCAAGATGCATTGCCATGGATGGAGATCTGTGTACTGTATGCCTAAGCGTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC