Sequence
atgc intronic sequence ATGC exonic sequencegtaagatgtcacatgattggcttgaaaggctcttatgttccatctttattctatgtagaaataataaatgtttcgtgcagCCAGAGAGTGTCCGTGAGATCACTGATCTTCTTGATGCTGTTGGGAACACCACAAAAGCAACAACGAAAGGGTTTGCCATTGGATCTGCTGCACTTGCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G78920.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G24120.4 (Glycine max), 3'ss of exon 9
---gtaagatgtcacatgatt-ggcttgaaaggctcttatgttccatctttattctatgtagaaataataaatgtttcgtgcagCCAGAGAGTGTCCGTGAGATCACTGATCTTCTTGATGCTGTTGGGAACACCACAAAAGCAACAACGAAAGGGTTTGCCATTGGATCTGCTGCACTTGCAT
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gtagttcttgctagaataatttggtccatagagttctttctgtgattcctcatgccatgtgtactgactattaacctttttcagCCTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACAACCAAAGCTACCACCAAAGGGTTTGCTATTGGTTCTGCTGCTCTTGCAT
upper sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 10
gtaagatgtcacatgattggcttgaa--aggctcttatgttcca---tctttattctatgtaga--aataataaatgtttcgtgcagCCAGAGAGTGTCCGTGAGATCACTGATCTTCTTGATGCTGTTGGGAACACCACAAAAGCAACAACGAAAGGGTTTGCCATTGGATCTGCTGCACTTGCAT
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gta-gttcttgctagaataatttggtccatagtgttatttctgagattcctcttgctatgtatactgactattaacctgtttt-cagCCTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACAACCAAAGCTACCACCAAAGGGTTTGCTATTGGTTCTGCTGCTCTTGCAT
upper sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 10
---------------gtaagatgtcacatgat-tggcttgaaaggctcttatgttccatctttattctatgtagaaataataaatgtttcgtgcagCCAGAGAGTGTCCGTGAGATCACTGATCTTCTTGATGCTGTTGGGAACACCACAAAAGCAACAACGAAAGGGTTTGCCATTGGATCTGCTGCACTTGCAT
| | | | || || | | |||| | || | || | | | ||| ||||| | | | ||||| || ||||| || ||||||||||||||||||||||| |||||||||||||||||||| || || || || || ||||||||||| || ||||| ||||
gtagccattctacaactgaatttttcaataatgttggctgaatcaaaaggaactttagtgctttgtttttaacttgatacaaaatgct-cttacagCCTGAAAGTGTTCGGGAGATCACTGATCTTCTTGATGCAGTTGGGAACACCACAAAAGCTACCACCAAGGGATTCGCCATTGGATCCGCGGCACTCGCAT
upper sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S105_42V6.1 (Physcomitrella patens), 3'ss of exon 11
------------gtaagatgtcacatgattggcttgaaaggctcttatgttc--catctttattc-----tatgtagaaataat------aaatgtttcgtgcagCCAGAGAGTGTCCGTGAGATCACTGATCTTCTTGATGCTGTTGGGAACACCACAAAAGCAACAACGAAAGGGTTTGCCATTGGATCTGCTGCACTTGCAT
|| | || |||| | || || | ||| | || | |||| | || | | || | || | |||||||||||||||| || |||||||||||| | || ||||| ||||| ||||| || |||||||| || ||||| |||||||| || || ||||| | || |
gtatgagtgtataggagcgattgcacttttggtat-aagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcagCCAGAGAGTGTTCGGGAGATCACTGATTTGCTGGATGCAGTTGGTAACACTACTAAAGCAACTACTAAAGGTTTTGCCATCGGCTCAGCTGCCTTAGCTT
upper sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S28_200V6.1 (Physcomitrella patens), 3'ss of exon 11
------------------------------gtaagatgtcacatgattggcttgaaaggctcttatgttccatctttattctatgtagaaataataaatgtttcg--tgcagCCAGAGAGTGTCCGTGAGATCACTGATCTTCTTGATGCTGTTGGGAACACCACAAAAGCAACAACGAAAGGGTTTGCCATTGGATCTGCTGCACTTGCAT
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gtgagggcgttcatgatttttttctatatcatgttctttggtgtaatgaactcgttgaacttttgtatttgggtgtcggcttcgttgattcctgttaacgtaatggttgcagCCACAAAATGTTCGAGAAATCACCGACTTGCTGGATGCCGTTGGCAACACCACTAAAGCAACAACCAAGGGTTTTGCCATTGGCTCAGCTGCCTTAGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaggctcttatgttccatctttattctatgtagaaataataaatgtttcgtgcagCCAGAGAGTGTCCGTGAGATCACTGATCTTCTTGATGCTGTTGGGAACACCACAAAAGCAACAACGAAAGGGTTTGCCATTGGATCTGCTGCACTTGCAT
tttattctatgtagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatgtcacatgattggcttgaaaggctcttatgttccatctttattctatgtagaaataataaatgtttcgtgcagCCAGAGAGTGTCCGTGAGATCACTGATCTTCTTGATGCTGTTGGGAACACCACAAAAGCAACAACGAAAGGGTTTGCCATTGGATCTGCTGCACTTGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC