Sequence
atgc intronic sequence ATGC exonic sequencegtaaacacaccatcttatcagtatatatgattgtaaaacccataatcattcatcttgtgtctttcatttttatctaacggttaaaacacagGTTGCTAGCGCAACAGCTACCTTTGTGATGATGTTTTCTTCGTCCTTATCCGTAGTCGAGTTCTATCTCCTCAAGAGATTCCCAATACCATACG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G36630.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G36630.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os03g51650.1 (Oryza sativa), 3'ss of exon 9
--gtaaacacac-catcttatcagtatatatgattgtaaaacccataatcat-tcatcttgtgtctttcatt-tttat----ctaacggttaaaacacagGTTGCTAGCGCAACAGCTACCTTTGTGATGATGTTTTCTTCGTCCTTATCCGTAGTCGAGTTCTATCTCCTCAAGAGATTCCCAATACCATACG
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ttataatcatttatgttatgtgattttcggcgttctttgccccttttttcctgttttgtcatttatttcactgtttgtgggattgtcatttatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG
upper sequence: AT2G36630.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G37360.1 (Glycine max), 3'ss of exon 9
gtaaacacaccatcttatcagtatatatgattgtaaaacccataatcattcatcttgtgtctttcatttttatctaacggttaaaacacagGTTGCTAGCGCAACAGCTACCTTTGTGATGATGTTTTCTTCGTCCTTATCCGTAGTCGAGTTCTATCTCCTCAAGAGATTCCCAATACCATACG
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--gtagggtgcatgtgcacgacacactttgatttggcattaatgttcaagcaacttgacttccaaggacgtgt-tgttgttcaaattgcagGTTGCTAGTGCTACAGCAACGTTTGTGATGATGTTTTCATCATCTTTGTCTGTGGTGGAATTCTACCTTCTCAAGAGGTTCCCCATTCCTTATG
upper sequence: AT2G36630.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G21310.2 (Glycine max), 3'ss of exon 9
------------gtaaacacaccatcttatcagtatatatgattgtaaaacc-----cataatcattcatcttgtgtctttcatttttatctaacggttaaaacacagGTTGCTAGCGCAACAGCTACCTTTGTGATGATGTTTTCTTCGTCCTTATCCGTAGTCGAGTTCTATCTCCTCAAGAGATTCCCAATACCATACG
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gtaaagtatatagtatatatgctctctcaattgagctaacactagttaaattaggagcataattctagaaacttaactttaaaagaatatttgatcataatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCAGTGGTTGAATTCTACCTTCTCAAGAGGTTCCCCATTCCTTATG
upper sequence: AT2G36630.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0007g04230.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------------------------------------gtaaacacaccatct--tatcagtatatatgattgtaaaacccataatcattcatcttgtgt---ctttcatttttatctaacggttaaaa------------cacagGTTGCTAGCGCAACAGCTACCTTTGTGATGATGTTTTCTTCGTCCTTATCCGTAGTCGAGTTCTATCTCCTCAAGAGATTCCCAATACCATACG
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gtatgtgactttgatgggtatctctaattgcaatggcctgtccaacctttgtacctgaacttagattacctgttataagaatcagaatttactactttctttgtcattctccgctaaaacacttacgatattataaaggaatgaataactgttggctttcacagGTTGCAAGCGCGACAGCAACTTTTGTGATGATGTTCTCATCATCCTTATCTGTTGTGGAGTTCTACCTCCTCAAGAGGTTTCCCATTCCATATGMapped 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|86073792|gb|DR369549.1|DR369549EST: GTGGATTTGTTCTCGGGCCTTTGCTTCTTGAGATTGGAGTCATCCCACAG GTTGCTAGCGCAACAGCTACCTTTGTGATGATGTTTTCTTCGTCCTTATCC
genomic: GTGGATTTGTTCTCGGGCCTTTGCTTCTTGAGATTGGAGTCATCCCACAGgtaaacacac ... taaaacacagGTTGCTAGCGCAACAGCTACCTTTGTGATGATGTTTTCTTCGTCCTTATCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacccataatcattcatcttgtgtctttcatttttatctaacggttaaaacacagGTTGCTAGCGCAACAGCTACCTTTGTGATGATGTTTTCTTCGTCCTTATCCGTAGTCGAGTTCTATCTCCTCAAGAGATTCCCAATACCATACG
atctaac putative branch site (score: 2)
tttcatttttatctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacacaccatcttatcagtatatatgattgtaaaacccataatcattcatcttgtgtctttcatttttatctaacggttaaaacacagGTTGCTAGCGCAACAGCTACCTTTGTGATGATGTTTTCTTCGTCCTTATCCGTAGTCGAGTTCTATCTCCTCAAGAGATTCCCAATACCATACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA