Sequence
atgc intronic sequence ATGC exonic sequence...gtccctgcgtaagaccaaaattatttaccatgtaacattgtaacctgtctctgaattgatcacttcacgattattgattgctgccaatcttctcttacagGGTCCTTCTATAGGCGATGTTGATGGTGACGGACACACGGAGGTTGTGGTTCCTACATCATCAGGAAACATATACGTTCTTAGTGGCAAGGATGGTTCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G09090.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g61050.1 (Oryza sativa), 3'ss of exon 9
-gtccctgcgtaagaccaaaattatttaccatgtaacattgtaacctgtctctgaattgatcacttcacgattattgatt-gctgccaatcttctcttacagGGTCCTTCTATAGGCGATGTTGATGGTGACGGACACACGGAGGTTGTGGTTCCTACATCATCAGGAAACATATACGTTCTTAGTGGCAAGGATGGTTCTA
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tagtattactatatgctttcactgtcttcactggtgcattc--agttttatttgggctatgcttttcataccctctgatttgccattgtcatatgatgacagCGCCCTACTGTTGGTGATGTTAATGGAGATGGTCGCACTGAAGTTGTGGTCCCAACCGTGTCAGGAAACATATATGTTCTTAGTGGAAAGGATGGCTCAA
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv08s0007g01790.t01 (Vitis vinifera), 3'ss of exon 9
-gtccctgcgtaagaccaaaattatttaccatgtaacattgtaacctgtctctgaattgatcacttcacgattattgattgctgccaatcttctcttacagGGTCCTTCTATAGGCGATGTTGATGGTGACGGACACACGGAGGTTGTGGTTCCTACATCATCAGGAAACATATACGTTCTTAGTGGCAAGGATGGTTCTA
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gggttgtgtctaggtgtatgatatgatatagtggttaaaggtgtttaaatgatctactgtttataccatactggcctgata-tacagaacacattcctcagGCTCCTACGATTGGCGATGTTGATGGGGATGGGCACACCGATGTTGTGGTTCCAACACTATCAGGAAATATATATGTTCTTAATGGCAAGGATGGATTACMapped 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|164132051|gb|ES011656.1|ES011656EST: CCAAGGAGTGGAAAATTTGGGAAGCACATCTTAAGAGCCTTGTTCCCCAG GGTCCTTCTATAGGCGATGT
genomic: CCAAGGAGTGG-AAATTTGGGAAGCACATCTTAAGAGCCTTGTTCCCCAGgtcaacaatt ... tctcttacagGGTCCTTCTATAGGCGATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtctctgaattgatcacttcacgattattgattgctgccaatcttctcttacagGGTCCTTCTATAGGCGATGTTGATGGTGACGGACACACGGAGGTTGTGGTTCCTACATCATCAGGAAACATATACGTTCTTAGTGGCAAGGATGGTTCTA
tattgat putative branch site (score: 3)
tcttctcttac putative PPT
attattgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtccctgcgtaagaccaaaattatttaccatgtaacattgtaacctgtctctgaattgatcacttcacgattattgattgctgccaatcttctcttacagGGTCCTTCTATAGGCGATGTTGATGGTGACGGACACACGGAGGTTGTGGTTCCTACATCATCAGGAAACATATACGTTCTTAGTGGCAAGGATGGTTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG