Sequence
atgc intronic sequence ATGC exonic sequence...tcttctctaagaaaggcctcccataaattttgtgtttggcttaggtagattatttgcaggtttgaggttctctaattaacttgtcttggtttgcttacagGACCAGTTCGATACCATTGATCTGTCTGATAACGAGATAGTTAAGCTAGAAAACTTCCCATACCTCAACCGTTTAGGAACTTTACTCATCAATAACAATC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09760.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G09760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G021742_T01 (Zea mays), 3'ss of exon 2
tcttctctaagaaaggcctcccataaattttgtgt----ttggcttaggtagattatttgcaggtttgaggttctctaatta--acttgtcttggtttgctt----acagGACCAGTTCGATACCATTGATCTGTCTGATAACGAGATAGTTAAGCTAGAAAACTTCCCATACCTCAACCGTTTAGGAACTTTACTCATCAATAACAATC
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----------gaatagtaaattttaaatcttatttagaatggtatttagttgtttgggttccttctctagcctttcttaacaccatctatattcactctctctctaacagGACCAGTTTGACACAATTGACTTGTCGGATAATGAGATTGTCAAGCTTGAAAACTTCCCATACTTGAATCGTCTTGGCACTCTACTAGTTAATAATAACA
upper sequence: AT1G09760.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 2
tcttctctaagaaaggcctcccataaattt-tgtgtttgg-----cttaggtagattatttgcaggtttgaggttctctaattaacttgtcttggtttgcttacagGACCAGTTCGATACCATTGATCTGTCTGATAACGAGATAGTTAAGCTAGAAAACTTCCCATACCTCAACCGTTTAGGAACTTTACTCATCAATAACAATC
|| ||| | | | | | |||| |||||| ||| || | || | ||| | || | | || | | || | | |||||||| || |||||||||||| ||||||| || ||||| || ||||| |||||||| || || || || || || || ||||| || ||||| ||||||
----ctttaaaattg--tttcagtggatttacttgtttgcagcttcttgtgttttgcactttaatgttgttgcttttgcatgatttttatatcggctcattggcagGACCAATTTGATACCATTGATTTGTCTGACAATGAGATTGTCAAGCTCGAAAACTTGCCTTATCTTAATCGGTTGGGTACTTTGCTTATCAACAACAATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagattatttgcaggtttgaggttctctaattaacttgtcttggtttgcttacagGACCAGTTCGATACCATTGATCTGTCTGATAACGAGATAGTTAAGCTAGAAAACTTCCCATACCTCAACCGTTTAGGAACTTTACTCATCAATAACAATC
aattaac putative branch site (score: 2)
tttgctt putative PPT
taattaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttctctaagaaaggcctcccataaattttgtgtttggcttaggtagattatttgcaggtttgaggttctctaattaacttgtcttggtttgcttacagGACCAGTTCGATACCATTGATCTGTCTGATAACGAGATAGTTAAGCTAGAAAACTTCCCATACCTCAACCGTTTAGGAACTTTACTCATCAATAACAATC
- - - -taagaaa
- - - - - - - - - - ccataaa
- - - - - - - - - - - - - - - - tgtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtttga