Sequence
atgc intronic sequence ATGC exonic sequenceAAGTCACACACGCTCTGTGTGAGATGTGGTCGCCGGAGCTTTCACATCCAGAAGAGTCGTTGCTCGGCATGTGCTTATCCAGCTGCCAGAAAGAGGACATgtatgtactctctctctatttctgtctctgtcttggaattttgggtctgatcatggagaattggagatatatgaaagagtcctggaatttatgattttgtgtgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G15250.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G15250.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA08G21960.1 (Glycine max), 5'ss of exon 2
AAGTCACACACGCTCTGTGTGAGATGTGGTCGCCGGAGCTTTCACATCCAGAAGAGTCGTTGCTCGGCATGTGCTTATCCAGCTGCCAGAAAGAGGACATgtatgtactctctctctatttctgtctctgtcttggaattttgggtctgatcatggagaattggagatatatgaaagagtcctggaatttatgattttgtgtgcag
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AAGACCCACACCCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCACCTCCAGAAGAGTCGTTGCTCTGCGTGCGCTTACCCCGCTGCGCGCACCAGGAAATgtaagt--tttttacttgttaaagtaatagggttcgtgtaaaaactcggtttttgaattgtttcgattgttccag-------------------------------
upper sequence: AT1G15250.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA15G01860.1 (Glycine max), 5'ss of exon 2
AAGTCACACACGCTCTGTGTGAGATGTGGTCGCCGGAGCTTTCACATCCAGAAGAGTCGTTGCTCGGCATGTGCTTATCCAGCTGCCAGAAAGAGGACATgtatgtactctctctctatttctgtctctgtcttggaattttgggtctgatcatggagaattggagatat-atgaaagagtcctggaatttatgattttgtgtgcag
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AAGACTCACACTCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCATCTCCAGAAGAGTCGTTGCGCCGCTTGTGCTTTCCCCGCCGCACGCACTAGGAAATgtaacttcttcttcttcaattatctcattagggtttatgtttggaattgttaacttac--tctgatttatgattaacgatttcag----------------------
upper sequence: AT1G15250.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA13G43450.1 (Glycine max), 5'ss of exon 2
AAGTCACACACGCTCTGTGTGAGATGTGGTCGCCGGAGCTTTCACATCCAGAAGAGTCGTTGCTCGGCATGTGCTTATCCAGCTGCCAGAAAGAGGACATgtatgtactctctctctatttctgtctctgtcttggaattttgggtctgatcatggagaattggagatatatgaaagagtcctggaatttatgattttgtgtgcag
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AAGACCCACACTCTCTGTGTGAGGTGTGGCCGCCGCAGCTTCCACCTCCAGAAGAGTCGCTGCGCCGCTTGTGCTTTCCCCGCTGCACGCACGCGGAAATgtaacttcttattcttctttccttcctcaattatcttatta-gggtttatgtttgga--attgttacccttactctttgatttatgattaacgatttcag------
upper sequence: AT1G15250.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA07G00700.1 (Glycine max), 5'ss of exon 2
AAGTCACACACGCTCTGTGTGAGATGTGGTCGCCGGAGCTTTCACATCCAGAAGAGTCGTTGCTCGGCATGTGCTTATCCAGCTGCCAGAAAGAGGACATgtatgtactctctctctatttctgtctctgtcttggaattttgggtctgatcatggagaattggagatatatgaaagagtcctggaatttatgattttgtgtgcag
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AAGACCCACACCCTCTGTGTGAGGTGTGGCCGCCGCAGTTTCCACCTCCAGAAGAGTCGTTGCGCCGCGTGCGCTTTCCCCGCTGCGCGCACCAGGAAATgtgagt--tttttacttactaaagtaaatg-----ggattgtg----taaaaattcggtctttgaattgtttgatgg--ttccag---------------------
upper sequence: AT1G15250.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S3_512V6.1 (Physcomitrella patens), 5'ss of exon 2
AAGTCACACACGCTCTGTGTGAGATGTGGTCGCCGGAGCTTTCACATCCAGAAGAGTCGTTGCTCGGCATGTGCTTATCCAGCTGCCAGAAAGAGGACATgtatgtactctc-tctctatttctgtctctgtc-ttggaattttgggtctgatcatggagaattggagatat-atgaaagagtcctggaatttatgattttgtgtgcag
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AAGTCCCACACGCTGTGCAGGCGTTGTGGCCGTAGAAGTTTTCACATCCAGAAGAGCCGTTGCTCGGCCTGTGCATACCCTGCCGCGAGAGTTCGCAGCTgtgagttctttcgtgactagctgtctctttttcatttgaagtcgagatcc--ttatgctgtctttattaggtcactcctcagcttctacacttgcaatgtcc-------
upper sequence: AT1G15250.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S83_87V6.1 (Physcomitrella patens), 5'ss of exon 2
AAGTCACACACGCTCTGTGTGAGATGTGGTCGCCGGAGCTTTCACATCCAGAAGAGTCGTTGCTCGGCATGTGCTTATCCAGCTGCCAGAAAGAGGACATgtatgtactctctctctatttctgtctctgtcttggaattttgggtctgatcatggagaattggagat-atatgaaagagtcctggaatttatgattttgtgtgcag
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AAGTCGCACACTCTGTGCAGGCGCTGTGGGCGGAGAAGTTTTCACATTCAGAAGAGCCGTTGCTCGGCATGTGCTTACCCTGCCGCTCGCGTTCGCTCTTgtacgtgacccctgacttagttgaacttt--ctacgatttttgtgcacg--tgttccgggtcgtcaatgattttacgtatttgtgaaatttagctcttaaagcg---
upper sequence: AT1G15250.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S475_18V6.1 (Physcomitrella patens), 5'ss of exon 2
AAGTCACACACGCTCTGTGTGAGATGTGGTCGCCGGAGCTTTCACATCCAGAAGAGTCGTTGCTCGGCATGTGCTTATCCAGCTGCCAGAAAGAGGACATgtatgtactctctctctatttctgtctctgtcttggaattttgggtctgatcatggagaattggagatatatgaaagagtcctggaatttatgattttgtgtgcag
|||||||||||||| || | | ||||| ||| | |||||||||||||||||||| || |||||||| ||||| || || || || ||| | | |||| || | || | || || |||| || || | | || | | | | || | | |||| |
AAGTCACACACGCTGTGCAGGCGCTGTGGCCGCAGAAGCTTTCACATCCAGAAGAGCCGCTGCTCGGCTTGTGCCTACCCTGCCGCGAGAGTTCGCAGCTgtaagtggctttcttcctggataattccttcattctaattaaggccggaattgtcttg--ttacctgccatcggtcgttatcagcccttcacggttttataa----
upper sequence: AT1G15250.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S152_133V6.1 (Physcomitrella patens), 5'ss of exon 2
AAGTCACACACGCTCTGTGTGAGATGTGGTCGCCGGAGCTTTCACATCCAGAAGAGTCGTTGCTCGGCATGTGCTTATCCAGCTGCCAGAAAGAGGACATgtatgtactctctctctatttctgtctctgtcttggaattttgggtctgatcatggagaattggagatatatgaaagagtcctggaatttatgattttg---tgtgcag-
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AAATCGCACACACTTTGTCGGCGATGTGGGCGTCGGAGCTTTCACATTCAGAAGAGCCGGTGCTCAGCATGTGCCTACCCCGCTGCAAGAGTCCGAAGCTgtatgtgaac-cactctatttgtcgtatttttttg---tttcaagt-tactcac-----atttttgttaccagaaatcatctcggaatacgtcgtctcaagatgtacgagMapped 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|19878800|gb|AU239631.1|AU239631EST: GAAGAGTCGTTGCTCGGCATGTGCTTATCCAGCTGCCAGAAAGAGGACAT ATAACTGGAGTGTGAAGGCAATAAGAAGAAAGACAACAGGAACTGGTAGGA
genomic: GAAGAGTCGTTGCTCGGCATGTGCTTATCCAGCTGCCAGAAAGAGGACATgtatgtactc ... ttgtgtgcagATAACTGGAGTGTGAAGGCAATAAGAAGAAAGACAACAGGAACTGGTAGGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAGTCACACACGCTCTGTGTGAGATGTGGTCGCCGGAGCTTTCACATCCAGAAGAGTCGTTGCTCGGCATGTGCTTATCCAGCTGCCAGAAAGAGGACATgtatgtactctctctctatttctgtctctgtcttggaattttgggtctgatcatggagaattggagatatatgaaagagtcctggaatttatgattttgtgtgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA