Sequence
atgc intronic sequence ATGC exonic sequencegtttgtagtttcataatctaccctaagttaaacgtcattgcacacaaacgtcattgcaaacgtcattgcacacaaacgtcatgtttattttcttggtgacaggattttgatactatgttctcatgtatagatgatttagatatctaatttgaggatctaaaatacatttgcagGTGATTGGTTTAAATAATGTCCCCATTGCTGGTGATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCAGAGGCACGTGCGGTATCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G17220.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os05g49970.2 (Oryza sativa), 3'ss of exon 8
gtttgtagtttcataatctaccctaagttaaacgtcattgcacacaaacgtcattgcaaacgtcattgcacacaaacgtcatgtttattttcttggtgacaggattttgatactatgttctcatgtatag-atgatt-tagatatct--aatttg--aggatctaaaatacatttgcagGTGATTGGTTTAAATAATGTCCCCATTGCTGGTGATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCAGAGGCACGTGCGGTATCAC
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-------------------------------------------------------------------------------gccttttactttagtaccattgagcattaaatgttcttcaaaagtttgtagtattattgtaagcatcctgaatttatcaagaaatgatatgttatgacagGTTATTGGCTTGAATAATGTACCCCTTGCTGGTGATGAATTTGAGTCTGTGGACAACCTTGATGTTGCACGTGAAAGGGCAAACGCACGTGCTGAAGCAC
upper sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G18580.1 (Glycine max), 3'ss of exon 9
gtttgtagtttcataatctaccctaagttaaacgtcattgcacacaaacgtcattgcaaacgtcattgcacacaaacgtcatgtttattttcttggtgacaggattttgatactatgttctcatgtatagatgatttagatatctaatttgaggatctaaaatacatttgcagGTGATTGGTTTAAATAATGTCCCCATTGCTGGTGATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCAGAGGCACGTGCGGTATCAC
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-------------------------------------------------------------gccactttttaagagc--catgtggattgtc--------gggctcttcatag-atgccaaaacttg-acctaattcaaagttatctgttgtgtcttctgtgcatgtccacagGTTATTGGGTTGAATAATGTTCCAATTGCTGGTGATGAATTTGAGGTTGTTGAATCCCTCGATACTGCACGTGAAAGGGCAGAGGCTCGTGCTGAGTCAT
upper sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G40370.1 (Glycine max), 3'ss of exon 8
gtttgtagtttcataatctaccctaagttaaacgtcattgcacacaaacgtcattgcaaacgtcattgcacacaaacgtcatgtttattttcttggtgacaggattttgatactatgttctcatgtatagatgatttagatatctaatttgaggatctaaaatacatttgcagGTGATTGGTTTAAATAATGTCCCCATTGCTGGTGATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCAGAGGCACGTGCGGTATCAC
|| | | | | || |||| | || ||| ||| || || | | ||| | | | | ||| | | | ||||| ||||| || |||||||| || ||||||||||||||||||||| | | ||||||||| || || || | |||||| | ||||| | |||
-----------------------------------------------------------------------tcagccactttttaagagccataattgtcaggctcttcataa-atgccaaaattta-acctaattcaaaattttctgttgtgtcctctgtgcttctctacagGTTATTGGATTGAATAATGTTCCAATTGCTGGTGATGAATTTGAGGTTATTGAATCCCTTGATACTGCACGTGAAAGGGCAGAAACTCGTGCTGAGTCAT
upper sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv19s0027g00130.t01 (Vitis vinifera), 3'ss of exon 8
gtttgtagtttcataatctaccctaagttaaacgtcattgcacacaaacgtcattgcaaacgtcattgcacacaaacgtcatgtttattttcttggtgacaggattttgatactatgttctcatgtatagatgatttagatatctaatttgaggatctaaaatacatttgcagGTGATTGGTTTAAATAATGTCCCCATTGCTGGTGATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCAGAGGCACGTGCGGTATCAC
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-------------------------------------------------------gaaaatgt-actaaatatggctgttatttgcatgatcat--ttgctgc-ttctgtgatagtgatctactgtgt---tcttctaaatttct--tctga---------atgctgctgtagGTCATTGGATTGAATAATGTTCCAATTGCTGGTGATGAATTTGAGGTCGTTGGCTCCCTTGATATTGCTCGAGAAAGAGCGGAGGCACGTGCAGAGTCATMapped 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|125029380|gb|EL101649.1|EL101649EST: GCTGGACCCTCCATACCTGTACAG GTGATTGGTTTAAATAATGTCCCCATTGCTGGTGATGAATTTGAGATCGTC
genomic: GCTGGACCCTCCATACCTGTACAGgtttgtagtt ... acatttgcagGTGATTGGTTTAAATAATGTCCCCATTGCTGGTGATGAATTTGAGATCGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcatgtatagatgatttagatatctaatttgaggatctaaaatacatttgcagGTGATTGGTTTAAATAATGTCCCCATTGCTGGTGATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCAGAGGCACGTGCGGTATCAC
atctaaa putative branch site (score: 3)
atttagatatctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtagtttcataatctaccctaagttaaacgtcattgcacacaaacgtcattgcaaacgtcattgcacacaaacgtcatgtttattttcttggtgacaggattttgatactatgttctcatgtatagatgatttagatatctaatttgaggatctaaaatacatttgcagGTGATTGGTTTAAATAATGTCCCCATTGCTGGTGATGAATTTGAGATCGTCTCTTCCCTTGATGTGGCGCGGGAGATGGCAGAGGCACGTGCGGTATCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG