Sequence
atgc intronic sequence ATGC exonic sequencegtaaagcacattcagggagcttagttgatccgcttgctatatagatttctgagaatccatgtgacgatttcagGTCGATGAGAAGGGCACAAGGTGGTTTTACACCGGAGATATTGGGAGATTCCACCCTGATGGATGTCTCGAAGTCATCGATAGAAAGAAAGATATTGTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G04350.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G04350.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G07280.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------gtaaagcacattcagggagcttagttgatccgcttgctatatagatttctgagaatccatgtgacgatttcagGTCGATGAGAAGGGCACAAGGTGGTTTTACACCGGAGATATTGGGAGATTCCACCCTGATGGATGTCTCGAAGTCATCGATAGAAAGAAAGATATTGTTA
| || || | | ||| | | || || | || || ||| | | | | | | ||||| |||||||| || | | |||||||| || || ||||||||| ||||||||||||||||||||| ||| |||| ||||| |||||||||||||| |
gtaatttcccaagttacagttgtatgcatgacatttttcctttttaatttcctttaactgctcttaaatctgtttttgcatatta-ctaagccactcgttacattttttttttgttttttaacttagta---cagGTTGATGAGAAAGGTATGCGCTGGTTTTATACTGGTGATATTGGGCAATTCCACCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA
upper sequence: AT2G04350.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G11700.1 (Glycine max), 3'ss of exon 9
-------------------------------------------gtaaagcacattcagggagctt--agttgatcc-gcttgctatataga---tttctgagaatccatgtgacgattt----cagGTCGATGAGAAGGGCACAAGGTGGTTTTACACCGGAGATATTGGGAGATTCCACCCTGATGGATGTCTCGAAGTCATCGATAGAAAGAAAGATATTGTTA
||| | || | ||| | ||| | || | || ||| || | | | | | || ||||| ||||||||||| | | |||||||| || || ||||||||| |||||| |||||||||||||| ||| |||| ||||| |||||||||||||| |
gtaatttccaaacttatagttgtatgcatgccatttttcctttataatttcctttaatttctctttaatttgcttttgcatattactaagacacttgttacatttttgttttttaacttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA
upper sequence: AT2G04350.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G07060.1 (Glycine max), 3'ss of exon 8
------------------------------------------gtaaagcacattcagggagcttagttgatccgcttgcta-tatagatttctgaga--atccatgtgacgatttcagGTCGATGAGAAGGGCACAAGGTGGTTTTACACCGGAGATATTGGGAGATTCCACCCTGATGGATGTCTCGAAGTCATCGATAGAAAGAAAGATATTGTTA
| || |||| || | | |||||| | || | | || || | | ||||| |||||| | || | | |||||||| || || ||||| || |||||| |||||||||||||| ||| |||| ||||| ||||| |||||||| |
gtaattttcaaactttcagttatatgcctattatctttcccttttaactttcttcaactgctctaaaatgtacctttgctaatgtatgccacatgggtcatttttgaacttagtacagGTTGATGAGCATGGTATGCGTTGGTTTTATACTGGGGATATCGGACAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAGGATATTGTCAMapped 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|164113349|gb|ES140545.1|ES140545EST: CAATCAAGAAAAAACCGATGAGGTTTACAAG GTCGATGAGAAGGGCACAAGGTGGTTTTACACCGGAGATATTGGGAGATTC
genomic: CAATCAAGAAAAAACCGATGAGGTTTACAAGgtaaagcaca ... acgatttcagGTCGATGAGAAGGGCACAAGGTGGTTTTACACCGGAGATATTGGGAGATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttagttgatccgcttgctatatagatttctgagaatccatgtgacgatttcagGTCGATGAGAAGGGCACAAGGTGGTTTTACACCGGAGATATTGGGAGATTCCACCCTGATGGATGTCTCGAAGTCATCGATAGAAAGAAAGATATTGTTA
agttgat putative branch site (score: 5)
tatatagattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagcacattcagggagcttagttgatccgcttgctatatagatttctgagaatccatgtgacgatttcagGTCGATGAGAAGGGCACAAGGTGGTTTTACACCGGAGATATTGGGAGATTCCACCCTGATGGATGTCTCGAAGTCATCGATAGAAAGAAAGATATTGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA