Sequence
atgc intronic sequence ATGC exonic sequenceCTTCCGGACCAAGGTTTATCACCCAAACATCAACAGTAATGGAAGTATCTGTCTTGACATTCTGAAAGAGCAGTGGAGCCCTGCACTTACCGTATCCAAGgtgatcaaattgtttcacttccttactttttagtatagcattagtctattttccaccacaccttcttgtgaccatgtcttagttaaatggtcatgtctta...
Basic information
species | Arabidopsis thaliana |
transcript | AT5G56150.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G56150.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os04g57220.1 (Oryza sativa), 5'ss of exon 4
CTTCCGGACCAAGGTTTATCACCCAAACATCAACAGTAATGGAAGTATCTGTCTTGACATTCTGAAAGAGCAGTGGAGCCCTGCACTTACCGTATCCAAGgtgatcaaattgtttcacttccttactttttagtatagcattagtctattttccaccacaccttcttgtgaccatgtcttagttaaatggtcatgtctta
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TTTCCGCACCAAGGTTTTCCACCCGAACATTAATAGCAATGGCAGCATTTGCCTCGACATCCTCAAGGAACAGTGGAGTCCTGCACTTACCATATCAAAGgtaattat-cagcatgacctgatt--tcaacattttggcccttctgtgacacctgatgaattgtgttatcatta-attctaacag---------------
upper sequence: AT5G56150.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G102471_T03 (Zea mays), 5'ss of exon 3
CTTCCGGACCAAGGTTTATCACCCAAACATCAACAGTAATGGAAGTATCTGTCTTGACATTCTGAAAGAGCAGTGGAGCCCTGCACTTACCGTATCCAAGgtgatcaaattgtttcacttccttactttttagtatagcattagtctattttccaccacaccttcttgtgaccatg---tcttagttaaatggtcatgtctta---
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TTTCCGCACCAAGGTTTTCCACCCGAACATCAACAGCAACGGCAGCATTTGCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgt----aaattgtctacattgtttatattgtgagttctggctgcactctgatccacctgaatcctccgaggttttgaggccttacttt--tggctccaccccaaca
upper sequence: AT5G56150.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G102471_T05 (Zea mays), 5'ss of exon 4
-----CTTCCGGACCAAGGTTTATCACCCAAACATCAACAGTAATGGAAGTATCTGTCTTGACATTCTGAAAGAGCAGTGGAGCCCTGCACTTACCGTATCCAAGgtgatcaaattgtttcacttccttactttttagtatagcattagtctattttccaccacaccttcttgtgaccat---gtcttagttaaatggtcatgtctta
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GTGTCTTTCCGCACCAAGGTTTTCCACCCGAACATCAACAGCAACGGCAGCATTTGCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATctcaaaggt----aaattgtctacattgtttatattgtgagttctggctgcactctgatccacctgaatcctccgaggttttgaggccttacttttggctccac------
upper sequence: AT5G56150.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G18310.1 (Glycine max), 5'ss of exon 4
CTTCCGGACCAAGGTTTATCACCCAAACATCAACAGTAATGGAAGTATCTGTCTTGACATTCTGAAAGAGCAGTGGAGCCCTGCACTTACCGTATCCAAGgtgatcaaattgtttcacttc-cttactttttagtatagcattagtctattttccaccacaccttcttgtgaccatgtcttagttaaatggtcatgtctta
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CTTCCGAACCAAGGTATTTCACCCTAACATAAACAGCAATGGAAGTATCTGTCTGGACATTCTGAAAGAGCAGTGGAGTCCTGCCCTTACAGTTTCCAAGgtattaggctttatacgtgtcattttccttgcctaacttcaccaatttgttttct-tgatgatttaatgcatcagtagatccttgaactttttaggaattt
upper sequence: AT5G56150.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv19s0015g01190.t01 (Vitis vinifera), 5'ss of exon 4
CTTCCGGACCAAGGTTTATCACCCAAACATCAACAGTAATGGAAGTATCTGTCTTGACATTCTGAAAGAGCAGTGGAGCCCTGCACTTACCGTATCCAAGgtgatcaaattgtttcacttccttactttttagtatagcattagtctattttccaccacaccttcttgtgaccatgtcttag--ttaaatggtcatgtctta
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CTTCAGAACAAAGGTGTTCCACCCCAACATTAACAGCAATGGTAGCATCTGCCTTGATATCCTGAAAGAGCAGTGGAGCCCTGCCCTCACAATATCCAAGgtaatttgcatctttaatacatttaatttataaagatgtttcccttagttgttcataagatggtaaatgaaccttactgtatacttccaaggtcccactt--Mapped 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|301501987|gb|HO207527.1|HO207527EST: GTCTTGACATTCTGAAAGAGCAGTGGAGCCCTGCACTTACCGTATCCAAG GTTCTTCTGTCGATATGCTCATTGCTGACGGATCCAAACCCTGACGATCCT
genomic: GTCTTGACATTCTGAAAGAGCAGTGGAGCCCTGCACTTACCGTATCCAAGgtgatcaaat ... atttccgcagGTTCTTCTGTCGATATGCTCATTGCTGACGGATCCAAACCCTGACGATCCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTTCCGGACCAAGGTTTATCACCCAAACATCAACAGTAATGGAAGTATCTGTCTTGACATTCTGAAAGAGCAGTGGAGCCCTGCACTTACCGTATCCAAGgtgatcaaattgtttcacttccttactttttagtatagcattagtctattttccaccacaccttcttgtgaccatgtcttagttaaatggtcatgtctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacttcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttcttg