Sequence
atgc intronic sequence ATGC exonic sequence...tcttattatgatcaagatcgatgatgctaagcactgttgcttctttgctttcttagttagtcattaagcctttatttgtgttctctctgactctctgcagCCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39890.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 1
tcttattatgatca-agatcgatgatgc-taagcactgttgcttctttgctttcttagttagtcattaagcctttatttgtgttctctctgactct--ctgcagCCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATG
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----atcttcttcgtaaatttgttttgcatttgaatctttacgatctcccttcccccttttcctgctagggtcttgacaaatttctagatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTG
upper sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 1
tcttattatgatcaagatcgatg-atgctaagcactgttgcttctttgctttcttagttagtcattaagcctttatttgtgttctctctgactct--ctgcagCCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATG
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---aattatcttcttcgtaaatttgttttgcacaatgtttccatctcccttcccccttttcctgctagggtcttgacaaatttcttgatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTG
upper sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 1
----tcttattatgatcaagatcgatgatgctaagcactgttgcttctttgctttcttagttagtcattaagcctttatttgtgtt-ctctctgactctctgcagCCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATG
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gtttccttggtat-atatttttttgttctgtcaaggatccacaatttttattcttcct-gctgctagatggctgacaaaatattttgttatctaaatttc---agGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTG
upper sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
tcttattatgatcaagatcgatgatgctaagcactgttgcttctttgctttcttagtt--agtcattaagcctttatttgtgttctctctgactctctgcagCCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATG
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-aaaaagaaaaaaaaaattggtttatctaggtaat-ctgtctattggagttaaaattttaaattagttacattctcttgatactcctttttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTGMapped 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|116437617|gb|EG480209.1|EG480209EST: CCAGCATCATCACTCGTTTCATGTATGACAAATTCGACACCACGTACCAG CCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGA
genomic: CCAGCATCATCACTCGTTTCATGTATGACAAATTCGACACCACGTACCAGgtatttacac ... ctctctgcagCCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctttcttagttagtcattaagcctttatttgtgttctctctgactctctgcagCCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATG
ctctgac putative branch site (score: 3)
ttctctctgactctct CT-rich tract
tttatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttattatgatcaagatcgatgatgctaagcactgttgcttctttgctttcttagttagtcattaagcctttatttgtgttctctctgactctctgcagCCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - atcaaga
- - - - - - - - - - - - - ctaagca
- - - - - - - - - - - - - - - - -ctgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctctct