Sequence
atgc intronic sequence ATGC exonic sequencegtatgagtatattagattaggccacttcttgactttgctctgattcgagatctctcaaggacatcttcttattatctacttgtgtgtttctttaaagATTTGGATTTCAGTTTTATGGAGATGAATCCTTTTACACTAGTCGATGGAGAACCATTCCCTCTGGATATGAGAGGAGAATTAGATGACACTGCTGCCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09430.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 4
-----gtatgagtatattagattaggccacttcttgactt--tgctctgatt-cgagatctctcaagga-catcttcttat------tatc--tacttgtgtgtttc-tttaaagATTTGGATTTCAGTTTTATGGAGATGAATCCTTTTACACTAGTCGATGGAGAACCATTCCCTCTGGATATGAGAGGAGAATTAGATGACACTGCTGCCTT
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gtattaaagatgcatatagaattcacttgtcatttgttgtaatgttttaattgtaaaatgtaataataagcgtattggtatatcatgtatccataataatatgctccctttacagACTTGGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT
upper sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g47330.1 (Oryza sativa), 3'ss of exon 4
-----gtatgagtatattagattaggccacttcttgactt--tgctctgattcgagatctctcaaggacatcttcttattatctacttgtg------tgtttct-ttaaagATTTGGATTTCAGTTTTATGGAGATGAATCCTTTTACACTAGTCGATGGAGAACCATTCCCTCTGGATATGAGAGGAGAATTAGATGACACTGCTGCCTT
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gtattaaagatgcatatagaattcacttttcatttgttgtaatgttttagttgtaaatgtaataaacgtattggtctatcatgtatccataacaatatgctcccattacagACTTAGATTTCTCATTTCTCGAGATGAACCCATTTACCATCGTGAATGGAGAGCCGTATCCTCTGGACATGAGAGGAGAATTAGATGACACAGCAGCTTT
upper sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 4
-------gtatgagtatattagattaggccacttcttgactttgctctgattcgagatctctcaaggacatcttcttattatctacttgtgtgtttctttaaagATTTGGATTTCAGTTTTATGGAGATGAATCCTTTTACACTAGTCGATGGAGAACCATTCCCTCTGGATATGAGAGGAGAATTAGATGACACTGCTGCCTT
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gtactcactcttgcttttcaaaggcagacagtttgtagttgttgcttt---tccag---tttcaaca----ctcaacataagatgctcattggttcttttgcagACTTGGATTTCTCATTTCTTGAGATGAACCCATTCACCTTGGTAAATGGTGAACCGTATCCTCTGGATATGAGAGGAGAACTAGATGACACAGCTGCTTT
upper sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 3'ss of exon 5
---gtatgagtata--ttagattaggccacttcttgactt-tgctctgattcgagatctctcaaggacatcttcttattatctacttgtgtgtttctttaaagATTTGGATTTCAGTTTTATGGAGATGAATCCTTTTACACTAGTCGATGGAGAACCATTCCCTCTGGATATGAGAGGAGAATTAGATGACACTGCTGCCTT
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tgtgtataatttttgttttcattcttctattttttgtttaacattttgttgagaacattgtcattgttcacttctaactgttgtaccat---tctctccacagATCTTGACTTCAGTTTCCTAGAGATGAACCCATTTACCCTGGTGAATGGGGAACCATACCCACTGGATATGAGGGGAGAATTGGATGATACTGCTGCTTTMapped 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|125301422|gb|EL315507.1|EL315507EST: TCGGCAACTTCATAATGGGTGCCTTTGCTGTATTTCAAG ATTTGGATTTCAGTTTTATGGAGATGAATCCTTTTACACTAGTCGATGGAG
genomic: TCGGCAACTTCATAATGGGTGCCTTTGCTGTATTTCAAGgtatgagtat ... ttctttaaagATTTGGATTTCAGTTTTATGGAGATGAATCCTTTTACACTAGTCGATGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcgagatctctcaaggacatcttcttattatctacttgtgtgtttctttaaagATTTGGATTTCAGTTTTATGGAGATGAATCCTTTTACACTAGTCGATGGAGAACCATTCCCTCTGGATATGAGAGGAGAATTAGATGACACTGCTGCCTT
ctctgat putative branch site (score: 4)
tgtttcttt putative PPT
ttcttattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagtatattagattaggccacttcttgactttgctctgattcgagatctctcaaggacatcttcttattatctacttgtgtgtttctttaaagATTTGGATTTCAGTTTTATGGAGATGAATCCTTTTACACTAGTCGATGGAGAACCATTCCCTCTGGATATGAGAGGAGAATTAGATGACACTGCTGCCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC