Sequence
atgc intronic sequence ATGC exonic sequencegtatgagtcatgagtggttcgaattatgcctatgttgtatctttgaattttcaagcttctataaaacttatcgtgtcttgcagCCAGAAAGTGTCCGTGAGATCACTGATGTTCTTGATGCTGTTGGGAATACCACAAAAGCAACAACAAAAGGGTTTGCTATTGGATCTGCTGCCCTTGCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G16780.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G24120.4 (Glycine max), 3'ss of exon 9
---gtatgagtcatgagtggttcgaattatgcctatgttgtatctttgaattttcaagct-tctataa-aacttatcgtgtcttgcagCCAGAAAGTGTCCGTGAGATCACTGATGTTCTTGATGCTGTTGGGAATACCACAAAAGCAACAACAAAAGGGTTTGCTATTGGATCTGCTGCCCTTGCAT
|| | | || | || | || ||| | ||| ||| | ||| || | | || ||| | | || ||||| ||||||||||| ||||| |||||||| |||||||| || || || || || ||||| || || ||||||||||||||||| |||||||| |||||||
gtagttcttgcta-gaataatttggtccata---gagttctttctgtgattcctcatgccatgtgtactgactattaacctttttcagCCTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACAACCAAAGCTACCACCAAAGGGTTTGCTATTGGTTCTGCTGCTCTTGCAT
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 10
---gtatgagtcatgagtggttcgaattatgcctatgttgtatctttgaattttcaagct-tctata---aaacttatcgtgtcttgcagCCAGAAAGTGTCCGTGAGATCACTGATGTTCTTGATGCTGTTGGGAATACCACAAAAGCAACAACAAAAGGGTTTGCTATTGGATCTGCTGCCCTTGCAT
|| | | || | || | || |||| | ||| || | || ||| | |||| | ||| | ||| || ||||| ||||||||||| ||||| |||||||| |||||||| || || || || || ||||| || || ||||||||||||||||| |||||||| |||||||
gtagttcttgcta-gaataatttggtccata---gtgttatttctgagattcctcttgctatgtatactgactattaacctgtttt-cagCCTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACAACCAAAGCTACCACCAAAGGGTTTGCTATTGGTTCTGCTGCTCTTGCAT
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 10
------gtatgagtcatgagtggttcgaattatgcctatgttgtatctttgaattttcaagcttc-tataaaacttatcgtg------tcttgcagCCAGAAAGTGTCCGTGAGATCACTGATGTTCTTGATGCTGTTGGGAATACCACAAAAGCAACAACAAAAGGGTTTGCTATTGGATCTGCTGCCCTTGCAT
| | ||| | ||| ||| ||| | ||| ||| |||| | | ||||| |||| ||||| |||||||| || |||||||||||| |||||||||| |||||||| ||||||||||| || || || || || || |||||||| || || || ||||
gtagccattctacaactgaatttttc-aataatgttggctgaatcaaaaggaactttagtgctttgtttttaacttgatacaaaatgctcttacagCCTGAAAGTGTTCGGGAGATCACTGATCTTCTTGATGCAGTTGGGAACACCACAAAAGCTACCACCAAGGGATTCGCCATTGGATCCGCGGCACTCGCAT
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S105_42V6.1 (Physcomitrella patens), 3'ss of exon 11
--------------------gtatgagtcatgagtggttcgaattatgcctatgttgtatctttgaattttcaagcttctataaaacttatc-gtgtcttgcagCCAGAAAGTGTCCGTGAGATCACTGATGTTCTTGATGCTGTTGGGAATACCACAAAAGCAACAACAAAAGGGTTTGCTATTGGATCTGCTGCCCTTGCAT
| | | | | | |||| || | | | |||| | ||| | || || || | |||||||||| ||||| || |||||||||||| | || ||||| ||||| || || || |||||||| || ||||| ||||| || || || |||||| | || |
gtatgagtgtataggagcgattgcacttttggtataagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcagCCAGAGAGTGTTCGGGAGATCACTGATTTGCTGGATGCAGTTGGTAACACTACTAAAGCAACTACTAAAGGTTTTGCCATCGGCTCAGCTGCCTTAGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctatgttgtatctttgaattttcaagcttctataaaacttatcgtgtcttgcagCCAGAAAGTGTCCGTGAGATCACTGATGTTCTTGATGCTGTTGGGAATACCACAAAAGCAACAACAAAAGGGTTTGCTATTGGATCTGCTGCCCTTGCAT
ttctataaaacttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagtcatgagtggttcgaattatgcctatgttgtatctttgaattttcaagcttctataaaacttatcgtgtcttgcagCCAGAAAGTGTCCGTGAGATCACTGATGTTCTTGATGCTGTTGGGAATACCACAAAAGCAACAACAAAAGGGTTTGCTATTGGATCTGCTGCCCTTGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC