Sequence
atgc intronic sequence ATGC exonic sequencegtatagtaaaagagtatagcatatatgggacctcttttactttttgtggatagtgtagttacattgcaatggtaattggtttgtgcagCAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55490.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 8
---gtatagtaaaagagtatagcatatatgggacctcttttactttttgtggatagtgt-agttacattgc--aatggtaattggtttgt-------gcagCAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAG
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tttctctattatgaggctgtatattgaatgtgttgt-ttgtacaagaaaagaaaagcatcagtcctgctcctgattgcttttttatctatccaatttgcagGCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAGCTTGCTGGTGGTGTTGCAGTCATTCAG
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 8
-------------------------------------------------------------------------------------------------gtatagtaaaagagtatagcatatatgggacctcttttactttt-----tgtggatagtgtagt-tacattgcaatggtaattggtttgtg--cagCAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAG
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gtctgtattatttaaaattaaaaattctatgtgttcctgtacttctcgtcaaaccactcctgtattcattttctcctgaccctgctcttttttgggggtttctttgcttacatgaatttacagggcagatcttttggattcacatgtctcagtatttttttgtggatttttatacaagttattttttcttcagGTTGCTGAACAGGAATATGAGAAAGAAAAACTGAATGAGAGAATAGCTAAGCTCTCTGGTGGTGTTGCTGTCATCCAG
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 2
--gtatagtaaaagagtatagcatatatgggacctcttttactttttgtggatagtgtagttacattgcaatggtaattggtttgtgcagCAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAG
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gtctctgaccttttcctgttctctttgttcactcgattttactgctcaggtgaaaatctgaaagtctgcttttatcaacctaatttttagGCAGCAGAACAAGAATATGAAAAGGAAAAGCTCAATGAGAGGATAGCAAAGCTTGCTGGTGGTGTTGCTGTCATTCAG
upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 8
----------gtatagtaaaagagtatagcatatatgggacctcttttactttttgtggatagtgtagttacattgcaatggtaattggtttgtgcagCAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAG
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gtatctatctgtcctctcactcactcacacacaca-gagagtaaatatgtgtttgctgaactttgttgat-ctttcttacat--atgtgttgattcagGCAGCAGAGCAAGAATATGAGAAGGAAAAACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGMapped 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|47832210|gb|CK121894.1|CK121894EST: CACAGGATGCAGTGAAAAAGCGTGTTACACAGATTAAAAATCTTATTGAG CAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAG
genomic: CACAGGATGCAGTGAAAAAGCGTGTTACACAGATTAAAAATCTTATTGAGgtatagtaaa ... gtttgtgcagCAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttactttttgtggatagtgtagttacattgcaatggtaattggtttgtgcagCAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAG
acttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagtaaaagagtatagcatatatgggacctcttttactttttgtggatagtgtagttacattgcaatggtaattggtttgtgcagCAAGCGGAGCAAGATTACGAGAAGGAGAAACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG