Sequence
atgc intronic sequence ATGC exonic sequencegtctatataacttactctcctgctgcagatcactgaatgttgataacctgattacactaacctgtgtgttttggttattttttctttcagCTACTCAGAAAACTGTTGATGGGCCATCAATGAAGGACTGGAGAGGAGGTCGGGGCGCTAGTCAAAACATCATTCCTAGCTCAACCGGCGCCGCGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79530.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 9
----------gtctatataacttactctcct----gctgcagatcactgaatgttgataacctgattacactaacctgtgtgtt--------ttggttattttttct---ttcagCTACTCAGAAAACTGTTGATGGGCCATCAATGAAGGACTGGAGAGGAGGTCGGGGCGCTAGTCAAAACATCATTCCTAGCTCAACCGGCGCCGCGAAG
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gttttctttcccttatgaattttgtcattgtcaaggatggagactgccaattttt--cagtctcctcatatcatgttgttcattagtcataacagacttgctttcctatattcagCCACCCAGAAGACTGTCGATGGCCCTTCAATGAAAGATTGGAGAGGAGGGCGTGGTGCTGCTCAAAACATAATTCCTAGCTCCACTGGTGCAGCCAAG
upper sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 9
-----------gtctatataacttactctcctgctgcagatcactgaatgttgata-acctgattacactaacctgtgtgttttggttattttttctt--tcagCTACTCAGAAAACTGTTGATGGGCCATCAATGAAGGACTGGAGAGGAGGTCGGGGCGCTAGTCAAAACATCATTCCTAGCTCAACCGGCGCCGCGAAG
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gttggttactggctttcatccagtgtctacctgtt--aagtcatttgccattttcatgcattttcaaaataattgtcatgagcatgttactgtaccatgtccagCCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAGMapped 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|124708344|gb|EH799746.1|EH799746EST: TCCACGCAACTACAG CTACTCAGAAAACTGTTGATGGGCCATCAATGAAGGACTTGGAGAGGAGGT
genomic: TCCACGCAACTACAGgtctatataa ... tttctttcagCTACTCAGAAAACTGTTGATGGGCCATCAATGAAGGACT-GGAGAGGAGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgttgataacctgattacactaacctgtgtgttttggttattttttctttcagCTACTCAGAAAACTGTTGATGGGCCATCAATGAAGGACTGGAGAGGAGGTCGGGGCGCTAGTCAAAACATCATTCCTAGCTCAACCGGCGCCGCGAAG
cactaac putative branch site (score: 1)
ttattttttctttc putative PPT
ttttggttatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctatataacttactctcctgctgcagatcactgaatgttgataacctgattacactaacctgtgtgttttggttattttttctttcagCTACTCAGAAAACTGTTGATGGGCCATCAATGAAGGACTGGAGAGGAGGTCGGGGCGCTAGTCAAAACATCATTCCTAGCTCAACCGGCGCCGCGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA