Sequence
atgc intronic sequence ATGC exonic sequence...agcgtcaatttttcattaactacacgaaggacaagttaaggaacagagtttgtgtgtgtttatgttcctttaatggtgaatattgttgtgtgttttacagGCAGAAGAGGAGCCGGTTTTGAGTAGCTTCTTGTATGCTAGTATCTTGTCGCATGACTGTTTAGAGCAAGCATTGAGTTTTGTTCTAGCTAACCGTCTCC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G35640.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G35640.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G048740_T03 (Zea mays), 3'ss of exon 1
agcgtcaatttttcat---taactacacgaaggacaagttaaggaacagagtttgtgtgtgtttatgttcctttaatggtgaatattgttg--tgtgttttacagGCAGAAGAGGAGCCGGTTTTGAGTAGCTTCTTGTATGCTAGTATCTTGTCGCATGACTGTTTAGAGCAAGCATTGAGTTTTGTTCTAGCTAACCGTCTCC
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-gtctcacctctttatgcatggtcatgtttgtcatagttttactgttata--ttg-gtaaactgatgg-ccggcagtgtgatggactgatggtcatgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCTCATGATTGCCTAGAGCGTGCATTGAGCTTCGTCCTTGCAAATAGGCTTG
upper sequence: AT4G35640.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G08930.1 (Glycine max), 3'ss of exon 1
agcgtcaatttttcattaactacacgaaggacaagttaaggaacagagtttgtgtgtgtttatgttcctttaatggtgaatattgttg-tgtgttttacagGCAGAAGAGGAGCCGGTTTTGAGTAGCTTCTTGTATGCTAGTATCTTGTCGCATGACTGTTTAGAGCAAGCATTGAGTTTTGTTCTAGCTAACCGTCTCC
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aacgggaatttgaaccttgtt-caccacgttgtagtagactaggcccttctgttagacccaattctcaattgttattactgattgatggtgttatgtgcagGCGGAGAAGGAGCCGATTCTGAGTAGCTTCTTGTACGCTAGCATTTTGGCGCATGATTGCTTGGAGCAAGCATTGGCGTTTGTCGCCGCTAATCGTCTCC
upper sequence: AT4G35640.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G22630.1 (Glycine max), 3'ss of exon 2
----------agcgtcaatttttcattaactacacgaaggacaagttaaggaacagagtttgtgtgtgtttatgttcctttaatggtgaatattgttgtgtgttttacagGCAGAAGAGGAGCCGGTTTTGAGTAGCTTCTTGTATGCTAGTATCTTGTCGCATGACTGTTTAGAGCAAGCATTGAGTTTTGTTCTAGCTAACCGTCTCC
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tgaaatatgcagt-tagatgattcattttgcatatttgatgagtgttagagaaca---tttacatgt-ttcatatgcatc--atgat--ataccattatttgtgt-gcagGCAGAAAAGGAGCCAATTTTGAGTAGCTTCTTCTATGCCACTATTCTGTCTCATGATTGCTTGGAGCAAGCATTGGCTTTTGCTCTTGCCAACCGACTCC
upper sequence: AT4G35640.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0210g00190.t01 (Vitis vinifera), 3'ss of exon 1
agcgtcaatttttcattaactacacgaaggacaagttaaggaacagagtttgtgtgtgtttatgttcctttaatggtgaatattgttgtgtgtt-ttacagGCAGAAGAGGAGCCGGTTTTGAGTAGCTTCTTGTATGCTAGTATCTTGTCGCATGACTGTTTAGAGCAAGCATTGAGTTTTGTTCTAGCTAACCGTCTCC
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ggtggtggtgtcggggtgttgggctggaagagaatttcgtttggaagaataatttgt-tatctgatcttgacatatttgttgctaccatgcaatgtttcagGCGGAGAAGGAGCCAATTCTAAGTAGCTTCTTGTATGCCAGTATTTTGTCCCATGACTGTTTAGAGCAAGCATTGGCATTTGTTCTTGCAAATCGACTTCMapped 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|19875710|gb|AU236541.1|AU236541EST: CTAGTTATGACCCAATTTGGGATTCTATAAGAGAAGAAGCTAAGCTTGAG GCAGAAGAGGAGCCGGTTTTGAGTAGCTTCTTGTATGCTAGTATCTTGTCG
genomic: CTAGTTATGACCCAATTTGGGATTCTATAAGAGAAGAAGCTAAGCTTGAGgttttctcct ... tgttttacagGCAGAAGAGGAGCCGGTTTTGAGTAGCTTCTTGTATGCTAGTATCTTGTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagtttgtgtgtgtttatgttcctttaatggtgaatattgttgtgtgttttacagGCAGAAGAGGAGCCGGTTTTGAGTAGCTTCTTGTATGCTAGTATCTTGTCGCATGACTGTTTAGAGCAAGCATTGAGTTTTGTTCTAGCTAACCGTCTCC
ctttaat putative branch site (score: 4)
aatattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcgtcaatttttcattaactacacgaaggacaagttaaggaacagagtttgtgtgtgtttatgttcctttaatggtgaatattgttgtgtgttttacagGCAGAAGAGGAGCCGGTTTTGAGTAGCTTCTTGTATGCTAGTATCTTGTCGCATGACTGTTTAGAGCAAGCATTGAGTTTTGTTCTAGCTAACCGTCTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - -acacgaa
- - - - - - - - - - - - - - - - - - - aggaaca
- - - - - - - - - - - - - - - - - - - - - - - agtttgt