Sequence
atgc intronic sequence ATGC exonic sequence...atccatgtcacctgtgtgtttcagatcacttgtttagctcgatgatttcgcaatacataatgttgtacctctgatctatttttttttcaatcattttcagGTTGTTGCTGTTAAACAACTAGACAGGAATGGTCTACAAGGTAACAGAGAATTTCTGGTAGAGGTTCTTATGCTCAGTCTTCTTCATCATCCCAACTTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13160.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13160.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G137468_T02 (Zea mays), 3'ss of exon 1
atccatgtcacctgtgtgtttcagatcacttgtttagctcgatga----tttcgcaatacataatgttgtacctctgatctatttttttttcaatcattttcagGTTGTTGCTGTTAAACAACTAGACAGGAATGGTCTACAAGGTAACAGAGAATTTCTGGTAGAGGTTCTTATGCTCAGTCTTCTTCATCATCCCAACTTAG
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-ttcataccttatgt-tctcgtattttgctatagtagatgcaaaaggagtatggggctggattaaaaaaaactgatggtttaaatgtgatt--gtttgctgcagGTTGTTGCTATAAAGCAGCTTAACAGGGATGGGCTTCAAGGAAACAGAGAATTTCTAGTAGAAGTTCTCATGCTCAGCTTACTACATCATCAAAACTTGG
upper sequence: AT5G13160.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G140095_T03 (Zea mays), 3'ss of exon 2
-------atccatgtcacctgtgtgtttcagatcacttgttta-gctcgatgatttcgcaatacataatgttgtacctctgatctatttttttttcaatcattttcagGTTGTTGCTGTTAAACAACTAGACAGGAATGGTCTACAAGGTAACAGAGAATTTCTGGTAGAGGTTCTTATGCTCAGTCTTCTTCATCATCCCAACTTAG
| | | | || | | | | || | | |||| | | || | || | | | || | || ||| |||||||||||| | || || || ||||| |||| || ||||| |||||||||||||| ||||| ||||| |||||||| | || ||||||| ||| | |
tttgctagtttactgaaagaatatgatgtacagtagatgcaaaagacaaatgaagctggattaaaaaagacagacggtttaatgtgattgtttgctg--------cagGTTGTTGCTATAAAGCAGCTTAACAGGGATGGGCTTCAAGGAAACAGAGAATTTCTAGTAGAAGTTCTCATGCTCAGCTTACTACATCATCAAAACCTGG
upper sequence: AT5G13160.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G47570.1 (Glycine max), 3'ss of exon 2
--------------------------------------------atccatgtcacctgtgtgtttcagatcacttgtttagctcgatgatttcgcaatacataa--tgttgtacctctgatctatttttttttcaatcattttcagGTTGTTGCTGTTAAACAACTAGACAGGAATGGTCTACAAGGTAACAGAGAATTTCTGGTAGAGGTTCTTATGCTCAGTCTTCTTCATCATCCCAACTTAG
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gtataaagtattcactttttatgattatttcatctacagggattgcaattctttaccttacctttcacaccactaaactaaagtgctgtcaactctatttttcaattaaagtgactcctaacatttgatcatttagctgta--cagATTGTTGCTGTCAAACAGTTAGACAAAAATGGTCTTCAGGGTAATCGGGAATTCCTTGTAGAGGTTCTCATGCTCAGTCTTCTACATCACCCTAACCTTG
upper sequence: AT5G13160.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G44580.2 (Glycine max), 3'ss of exon 2
atccatgtcacctgtgtgtttcagatcacttgtttagctcgatgatttcgcaatacataatgttgtacctctgatctatttttttttcaatcattttcagGTTGTTGCTGTTAAACAACTAGACAGGAATGGTCTACAAGGTAACAGAGAATTTCTGGTAGAGGTTCTTATGCTCAGTCTTCTTCATCATCCCAACTTAG
|| |||| || || |||| | || | | | || | || | | | | ||| ||| |||||||| ||||||||||| ||||||| | ||||| || ||||| | ||||| || || |||||||| |||||||||||||| || || || || | |
---------------gtatttcttttc-tttctttaattaaattaacttaatttgaattaaattaaatttgtttttcgtttgcctttt-----ccaacagGTTGTGGCTGTTAAACAGTTAGACAGAGACGGTCTTCAGGGTAATCGGGAATTCCTCGTTGAGGTTCTCATGCTCAGTCTTCTACACCACCCTAATCTTG
upper sequence: AT5G13160.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0146g00250.t01 (Vitis vinifera), 3'ss of exon 2
atccatgtcacctgtgtgtttcaga--tcacttgtttagctcgat--gatttcgcaatacataatgttgtacctctgatctatttttttttcaatcattttcagGTTGTTGCTGTTAAACAACTAGACAGGAATGGTCTACAAGGTAACAGAGAATTTCTGGTAGAGGTTCTTATGCTCAGTCTTCTTCATCATCCCAACTTAG
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----ttttagcatgaatattgtagaatttagccactcaatcttgtttaattttgatagtggtgaagatgcattcatgtgataaagccatgtttgtctttctcagGTTGTTGCTGTTAAACAATTGGATAGAGAGGGTCTCCAGGGTAACAGGGAATTCCTGGTGGAGGTTCTCATGCTCAGCCTTCTGCATCACCCTAACCTAGMapped 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|116483438|gb|EG526030.1|EG526030EST: AAGGTGGATTTGGACGTGTCTACAAAGGAAGGCTTGACAGCACCGGTCAG GTTGTTGCTGTTAAACAACTAGACAGGAATGGTCTACAAGGTAACAGAGAA
genomic: AAGGTGGATTTGGACGTGTCTACAAAGGAAGGCTTGACAGCACCGGTCAGgtattttttg ... tcattttcagGTTGTTGCTGTTAAACAACTAGACAGGAATGGTCTACAAGGTAACAGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcgcaatacataatgttgtacctctgatctatttttttttcaatcattttcagGTTGTTGCTGTTAAACAACTAGACAGGAATGGTCTACAAGGTAACAGAGAATTTCTGGTAGAGGTTCTTATGCTCAGTCTTCTTCATCATCCCAACTTAG
ctctgat putative branch site (score: 4)
tttttttttcaatc putative PPT
atctatttttttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atccatgtcacctgtgtgtttcagatcacttgtttagctcgatgatttcgcaatacataatgttgtacctctgatctatttttttttcaatcattttcagGTTGTTGCTGTTAAACAACTAGACAGGAATGGTCTACAAGGTAACAGAGAATTTCTGGTAGAGGTTCTTATGCTCAGTCTTCTTCATCATCCCAACTTAG
- - - - - - - - - - - - - - - tgtttag
- - - - - - - - - - - - - - - - - - - - - - - - - caataca