Sequence
atgc intronic sequence ATGC exonic sequencegtatgcattgtctttgccgtttctgttacatatgtgaatgtcttaatgctattcgtggaattgagcatgattgtaatcattgtgtacgtttcgcttgcagAATCGCAGAGTGCTTTGCGTTTCTTGTTTGTACAAAATGGTCTAATCCAGTGATTCATAGAAGCTCACGTGATAGAGAAACTGGGTCATCTTCTACCAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73950.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73950.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g49900.1 (Oryza sativa), 3'ss of exon 7
gtatgcattgtctttgccgtttctgttacatatgtgaatgtcttaatgctattcgtggaattgagcatgattgtaatcattgtgtacgtttcgcttgcagAATCGCAGAGTGCTTTGCGTTTCTTGTTTGTACAAAATGGTCTAATCCAGTGATTCATAGAAGCTCACGTGATAGAGAAACTGGGTCATCTTCTACCAAT
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---------------gtgagactagtctcaatagcaattttctt-----tattaacgagatctgttataatataatccagcaccttcttttt-tgtacagAATCGCGGAGTGTTTTGCATTTCTTGTTTGTACTAGATGGTTTAATCCCATGATTCATAAATCTCCTAATCCTGGGGAGGCTAGCTCATCATCAGCGGCA
upper sequence: AT1G73950.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G13040.1 (Glycine max), 3'ss of exon 7
---gtatgcattgtctttgccgtt------tctgttacatatgtgaat-gtcttaatgctattcgtggaattgagcatgattgtaa--tcattgtgtacgtttcgcttgcagAATCGCAGAGTGCTTTGCGTTTCTTGTTTGTACAAAATGGTCTAATCCAGTGATTCATAGAAGCTCACGTGATAGAGAAACTGGGTCATCTTCTACCAAT---
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gtaggtttctttgtcttaagtgctaaaaaatgcattttgttaataagttgtgtttgttaaaatactgacatgaaagctttatataaggtttttatgacctataattttgcagTATTGCCGAGTGCTTTGCTTTCCTTGTATGTACAAAGTGGTCCAATCCAGTCATTCATAGAAATTCAAGAGA---AGCCAGTAGTTCATCTTCAACTACGATT
upper sequence: AT1G73950.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G07960.1 (Glycine max), 3'ss of exon 7
---gtatgcattgtctttgccgtt------tctgttacatatgtgaat-gtcttaatgctattcgtggaattga-gcatgattgtaatcattgtgtacgtttcgcttgcagAATCGCAGAGTGCTTTGCGTTTCTTGTTTGTACAAAATGGTCTAATCCAGTGATTCATAGAAGCTCACGTGATAGAGAAACTGGGTCATCTTCTACCAAT---
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gtaggtttctttgtcttaagtgctaaaaaatgcattttgttaataagttgtgtttgttaaaatgctgacatgaaagctttatataaggttttatgacctataattttgcagTATTGCCGAGTGCTTTGCTTTCCTTGTATGTACAAAGTGGTCCAATCCCGTCATTCATAGAAATTCAAGAGA---AGCTAGTAGTTCATCTTCAACTACGATT
upper sequence: AT1G73950.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv17s0000g04160.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------------------gtatgcattgtctttgccgtttctgttacat--atgtgaatgtcttaatgctattcgtggaattgagcatgattgtaatcattgtgt-acgtttcgcttgcagAATCGCAGAGTGCTTTGCGTTTCTTGTTTGTACAAAATGGTCTAATCCAGTGATTCATAGAAGCTCACGTGATAGAGAAACTGGGTCATCTTCTACCAAT
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gtatgtacctcacaagttcatgtttttcttttcttttcttttttggtttcttttactttaatattgtctagagcagtgatgtgaatagtttcttcatgcttttgaatgagagaaagaa-atgatgaatgtgtcatgttcttttaacagCATTGCAGAGTCCTTTGCCTTCCTTGTTTGTACAAAGTGGTCTAATCCAGTGATCCATAGAAATTCTCACACAACAGAAGCTGGTTCATCTTCTACAACTMapped 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|125199463|gb|EL214417.1|EL214417EST: CGATGTAGCTGCTCTTGGCTGGTGGGATTTATTCATTAATTTCGG AATCGCAGAGTGCTTTGCGTTTCTTGTTTGTACAAAATGGTCTAATCCAGT
genomic: CGATGTAGCTGCTCTTGGCTGGTGGGATTTATTCATTAATTTCGGgtatgcattg ... tcgcttgcagAATCGCAGAGTGCTTTGCGTTTCTTGTTTGTACAAAATGGTCTAATCCAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgctattcgtggaattgagcatgattgtaatcattgtgtacgtttcgcttgcagAATCGCAGAGTGCTTTGCGTTTCTTGTTTGTACAAAATGGTCTAATCCAGTGATTCATAGAAGCTCACGTGATAGAGAAACTGGGTCATCTTCTACCAAT
tcttaat putative branch site (score: 3)
tttcgctt putative PPT
attgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcattgtctttgccgtttctgttacatatgtgaatgtcttaatgctattcgtggaattgagcatgattgtaatcattgtgtacgtttcgcttgcagAATCGCAGAGTGCTTTGCGTTTCTTGTTTGTACAAAATGGTCTAATCCAGTGATTCATAGAAGCTCACGTGATAGAGAAACTGGGTCATCTTCTACCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA