Sequence
atgc intronic sequence ATGC exonic sequenceAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAGgtaaaacacatatgaaaacttttgagttgtgaattgtggcgttgggaagtatactgagatttattcttttggaatctttag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G40550.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G40550.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM5G862959_T04 (Zea mays), 5'ss of exon 7
AGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGG-------AAGCGGTCAGAGgtaaaacacatatgaaaacttttgagttgtgaattgtggcgttgggaagtatactgagatttattcttttggaatctttag----------
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GTATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagggtcaagttcct-tcctatctgtccttttttagttccttgtatctgaacagttgatgaaattagctccaataattttctccaaatattcaac
upper sequence: AT5G40550.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM5G862959_T01 (Zea mays), 5'ss of exon 6
------------------------------------------------AGT-TGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGG-------AAGCGGTCAGAGgtaaaacacatatgaaaacttttgagttgtgaattgtggcgttgggaagtatactgagatttattcttttggaatctttag----------
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TGACCATCATCCTGTAAGTATCACTCATTTAATATTGATGCACGTGCAGGTATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAAgtatgtgagggtcaagttcct-tcctatctgtccttttttagttccttgtatctgaacagttgatgaaattagctccaataattttctccaaatattcaac
upper sequence: AT5G40550.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA16G07460.1 (Glycine max), 5'ss of exon 6
AGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAGgtaa---aacacatatgaaaacttttgagttgtgaattgtggcgttgggaagtatactgagatttattcttttggaat----ctttag---------------------------------------------------------------------------------------------
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ATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCAAAGgtaacctaacctattaggaaatttgtcatgtttaaattatctagaatgctcatgccatgtacttgatttgcttgaggtgctactttaaacttacatgggaatttctttccacatgtcttgcattgttactgcatttgaatgacatgtttattttcattggtttctcctgctgcattcacag
upper sequence: AT5G40550.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA19G08050.2 (Glycine max), 5'ss of exon 7
AGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAGgtaa---aacacatatgaaaacttttgagttgtgaattgtggcgttgggaagtatactgagatttattcttttggaat----ctttag-------------------------------------------------------------------------------------------
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ATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCAAAGgtaacctaacctattaggaaatttgtcatgttt-aattatctagagtgctcatgtcatgtacttgatttacttgaggcgctactttaaacttaaatgggaatttctttccacatgtcttccattgtcacgcatttgaatgacgtgtttactttcatttgtgttcctgctgcattcacag
upper sequence: AT5G40550.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv14s0066g00210.t01 (Vitis vinifera), 5'ss of exon 7
AGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAGgtaa-aacacatatga--aaacttttgagttgtgaattgtggcgttgggaagtatactgagatttattcttttggaatctttag----------------
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ATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAGgtaataatctatataatggaaatctgacattatttagttatatattgttgccattgaagtgacatgatttcacaagatcagcaactgatgtactagatttMapped 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|164195652|gb|ES099415.1|ES099415EST: GAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAG GACCTATAAGTTGCCAATGTCATGCATTTTACCATT
genomic: GAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAGgtaaaacaca ... gaatctttagGACCTATAAGTTGCCAATGTTATGCATTTTACCATT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAGgtaaaacacatatgaaaacttttgagttgtgaattgtggcgttgggaagtatactgagatttattcttttggaatctttag
- - - - - - - TGAAGA
- - - - - - - - AAGAAC
- - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - AAGGAA