Sequence
atgc intronic sequence ATGC exonic sequencegtatgccatttacttcaaattcacaatcattttgcaaatttcatttgtttctgattacgattgttggatatgttttagATAAGGAAAATGAAAGGGCTGAAGCAGAAGAAGGCACATCTGAATGAGATTCAGATCAATGGTGGAGATATAGCAAAGAAAGTTGACTATGCCTGCAGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G61580.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g06750.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------------gtatgccatttacttcaaattcacaatcattttgcaaatt-tcatttgtttctgattacgattgttggatatgttttagATAAGGAAAATGAAAGGGCTGAAGCAGAAGAAGGCACATCTGAATGAGATTCAGATCAATGGTGGAGATATAGCAAAGAAAGTTGACTATGCCTGCAGTT
||| | || | | | | || || | || ||||| | || |||| ||| | | || || || || |||| ||||||||||| || |||||||||||||||| || || | ||||| |||||||||||||| || || | || || ||||||| | || |
gtcagtaacctactgttattttactatcttgtattttgagcccttctattcagttaattggatggtaaccat-gtgctgtaaattgtttgttcattctcattctaaatcttt-atgtgcttcagATTAGGAAAATGAAGGGCTTGAAGCAGAAGAAGGCTCACCTCATGGAGATCCAGATCAATGGTGGTACCATTGCCGATAAGGTGGACTATGGATACAAGT
upper sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G109677_T04 (Zea mays), 3'ss of exon 5
---------------gtatgccatttacttcaaat-tcacaatcattttgcaaatttcatttgtttctgattacgattgttggatat------gttttagATAAGGAAAATGAAAGGGCTGAAGCAGAAGAAGGCACATCTGAATGAGATTCAGATCAATGGTGGAGATATAGCAAAGAAAGTTGACTATGCCTGCAGTT
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gagtgaagtacacctatctttcatataattgaaaagtgattattttttctgaggcactaggtattagcaaactcacctcttatgtatttgtatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTATGGCTACAAAT
upper sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G324314_T05 (Zea mays), 3'ss of exon 4
---------------gtatgccatttacttcaaat-tcacaatcattttgcaaatttcatttgtttctga--ttacgattgttggat----atgttttagATAAGGAAAATGAAAGGGCTGAAGCAGAAGAAGGCACATCTGAATGAGATTCAGATCAATGGTGGAGATATAGCAAAGAAAGTTGACTATGCCTGCAGTT
| | ||| || || ||| | | || ||| | | | || | | || || || || || |||||||| ||||| ||||| || |||||||||||||||| || |||| ||||||||| |||||||||| || || | || || ||||||| || || |
gagtgaagtacacctatctttcatataattgaaaagtgattattttttctgaggcactaggtattagcaaactcaccttttatgtatttgtatattttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTATGGCTACAAAT
upper sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G801409_T04 (Zea mays), 3'ss of exon 3
----------------gtatgccatttacttcaaat-tcacaatcattttg------caaatttcatttgtttctgattacgattgttggatatgttttagATAAGGAAAATGAAAGGGCTGAAGCAGAAGAAGGCACATCTGAATGAGATTCAGATCAATGGTGGAGATATAGCAAAGAAAGTTGACTATGCCTGCAGTT
| | || || ||| | | || || || | | | | || | | || | ||| |||||||| ||||| ||||| || |||||||||||||||| || |||| ||||||||| |||||||||| || || | || || ||||||| || || |
tcaattccagtgatccaaacggggcgtaattgaaaagtgattatttttctgaggcactaggtattagcaaactcacctcttatgtatttg-tatcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTATGGCTACAAAT
upper sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G135727_T03 (Zea mays), 3'ss of exon 4
-------------gtatgccatttacttcaaa-ttcacaatcattttgcaaatttcatttgtt--tctgattacgattgttggatat------gttttagATAAGGAAAATGAAAGGGCTGAAGCAGAAGAAGGCACATCTGAATGAGATTCAGATCAATGGTGGAGATATAGCAAAGAAAGTTGACTATGCCTGCAGTT
| | ||| || || ||| || | | ||| | | | || | | | | ||| ||| |||||||| ||||| ||||| || |||||||||||||||| || |||| ||||||||| |||||||||| || || | || || ||||| | || | |
gggaagtaggcctatctttcatataattgaaaattgatttttttttctgaggcactaggtattagccaactctcacctcttgtgtatttctttcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTATAAAT
upper sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G132968_T02 (Zea mays), 3'ss of exon 4
------------gtatgccatttacttcaaa-ttcacaatcattttgcaaa--------tttcatttgtttctgattacgattgt-tggatatgttttagATAAGGAAAATGAAAGGGCTGAAGCAGAAGAAGGCACATCTGAATGAGATTCAGATCAATGGTGGAGATATAGCAAAGAAAGTTGACTATGCCTGCAGTT
| | ||| || || ||| || | || |||| | | | | ||| | | ||| | | | |||||||| ||||| ||||| || |||| ||||||||||| || |||| ||||||||| |||||||||| || || | || || ||||| | || || |
ggaagtaggtctatctttcatataattgaaaattgattatttttttctgaggcactaggtattagccaactctcacctcttgtgtatttgtttcttttagATTAGGAAGATGAAGGGTTTGAAACAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTACAAAT
upper sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0035g01020.t01 (Vitis vinifera), 3'ss of exon 3
-------------------gtatgccattta----cttcaaatt-cacaatcattt-tgcaaatt-----tcatttgtttctgat-tacgat-tgttggatatgttt-tagATAAGGAAAATGAAAGGGCTGAAGCAGAAGAAGGCACATCTGAATGAGATTCAGATCAATGGTGGAGATATAGCAAAGAAAGTTGACTATGCCTGCAGTT
| || ||| | ||| | || |||| | || ||||| || | ||||| |||| || | | | | || ||| ||||| || |||||||| || ||||||||||| ||||| || || | ||||||||| | |||||||||||| | || ||||| ||||||||||||| |||
gtagttttccatcaccaatatttgggattcaaagactttaggtttcacatttataaatgcaagttaccaattatttggcactgacatatcctatatggaatggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATTCAGGTGAATGGTGGAGATGTTGCTAAGAAGGTTGACTATGCCTATGGTTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|125242948|gb|EL257033.1|EL257033EST: GAAGATGAAGAAGTACTGCTCTGTCATCAGAGTTCTTGCTCACACTCAG ATAAGGAAAATGAAAGGGCTGAAGCA
genomic: GAAGATGAAGAAGTACTGCTCTGTCATCAGAGTTCTTGCTCACACTCAGgtatgccatt ... tatgttttagATAAGGAAAATGAAAGGGCTGAAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatcattttgcaaatttcatttgtttctgattacgattgttggatatgttttagATAAGGAAAATGAAAGGGCTGAAGCAGAAGAAGGCACATCTGAATGAGATTCAGATCAATGGTGGAGATATAGCAAAGAAAGTTGACTATGCCTGCAGTT
ttctgat putative branch site (score: 3)
aaatttcatttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgccatttacttcaaattcacaatcattttgcaaatttcatttgtttctgattacgattgttggatatgttttagATAAGGAAAATGAAAGGGCTGAAGCAGAAGAAGGCACATCTGAATGAGATTCAGATCAATGGTGGAGATATAGCAAAGAAAGTTGACTATGCCTGCAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG