Sequence
atgc intronic sequence ATGC exonic sequence...cctgaaaattgccaaaggaatttgtgctattttaaaacatagaacattaaactgctaaagttgtggccttattcttgtcacatttggctcgtgcaactagGCGTTGAAGCTTGAAGAATTTGGGGTGGAAGGCTCAGATGCTGAAAATGTTTGTTACTTACGAGATCTAGCTGATGCAAATAGGCTTGCCACTGTGATTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G27820.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G27820.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G07970.1 (Glycine max), 3'ss of exon 4
cctgaaaattgccaaaggaatttgtgctattttaaaacatagaacattaaactgctaaagttgtg-gccttattcttgtcacatttggctcgtgcaac--------tagGCGTTGAAGCTTGAAGAATTTGGGGTGGAAGGCTCAGATGCTGAAAATGTTTGTTACTTACGAGATCTAGCTGATGCAAATAGGCTTGCCACTGTGATTC
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--------atactaaatacatac-taatgatggaagaatttgaggatagcatacctacccccctttgctttctttacagtatatttaacacatgcaatgtcaattgtagGCTTTGAAGCTGGAAGAATTTGGGGTGAGTGGATCAGATGCAGAAAATGTATGTTATTTAAGACATATAGCAGATGCAAATAGGCTTGTAGATGTTATGC
upper sequence: AT3G27820.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G14500.1 (Glycine max), 3'ss of exon 4
cctgaaaattgccaaaggaatttgtgctattttaaaacata-gaacattaaactgctaaagttgtggccttattcttgtcacatttggctcgtgcaac--------tagGCGTTGAAGCTTGAAGAATTTGGGGTGGAAGGCTCAGATGCTGAAAATGTTTGTTACTTACGAGATCTAGCTGATGCAAATAGGCTTGCCACTGTGATTC
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--------tttgtaatgcaatatcactgcctttaaaagagatgtgaattctattacttcc-tagtaaccatttttacgggatattaaacacatgcaatgtcaattgtagGCTTTGAAGCTGGAAGAATTTGGGGTCACTGGATCAGATGCAGGAAATGTCTGTTATTTAAGAGATATAGCAGATGCAAATAGGCTTGTTGATGTTATGC
upper sequence: AT3G27820.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0066g01100.t01 (Vitis vinifera), 3'ss of exon 4
-----cctgaa--aattgccaaaggaatttgtgctattttaaaacatagaacattaaactgctaaagttgtggccttattcttgtcacatttggctcgtgcaactagGCGTTGAAGCTTGAAGAATTTGGGGTGGAAGGCTCAGATGCTGAAAATGTTTGTTACTTACGAGATCTAGCTGATGCAAATAGGCTTGCCACTGTGATTC
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atttataaggaccaattattgaggctaattctcacctattaaag-atagtg-atttaattaataat-ttgttgactga--ctaatcaattgcatcttatgta--tagGCATTGCAGCTTGAAGAATTTGGAGTGGCTGGATCAGATGCTGAAAATGTGTGTTATTTACGTGACTTGGCTGATGCCACCAGGCTTGTTGATGTCATGA
upper sequence: AT3G27820.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0014g05380.t01 (Vitis vinifera), 3'ss of exon 3
-----cctgaa--aattgccaaaggaatttgtgctattttaaaacatagaacattaaactgctaaagttgtggccttattcttgtcacatttggctcgtgcaactagGCGTTGAAGCTTGAAGAATTTGGGGTGGAAGGCTCAGATGCTGAAAATGTTTGTTACTTACGAGATCTAGCTGATGCAAATAGGCTTGCCACTGTGATTC
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atttataaggaccaattattgaggccaattctcacctattaaag-atagtg-atttaattaataat-ttgttgactga--ctaatcaattgcatcttatgta--tagGCATTGCAGCTTGAGGAATTTGGAGTGGCTGGATCAGATGCTGAAAATGTGTGTTATTTACGTGACTTGGCTGATGCCACCAGGCTTGTTGATGTCATGCMapped 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|125298295|gb|EL312380.1|EL312380EST: TCTTGATCATTGCAACAGGTGCCCGG GCGTTGAAGCTTG-AGAATTTGGGGTGGAAGGCTCAGATGCTGAAAATGTT
genomic: TCTTGATCATTGCAACAGGTGCCCGGgtatggcttg ... gtgcaactagGCGTTGAAGCTTGAAGAATTTGGGGTGGAAGGCTCAGATGCTGAAAATGTT
EST:
gi|124844268|gb|EH928705.1|EH928705EST: TCTTGATCATTGCAACAGGTGCCCGG GCGTTGAAGCTTGAAGAATTTGGGGTGGAAGGCTCAGATGCTGAAAATGTT
genomic: TCTTGATCATTGCAACAGGTGCCCGGgtatggcttg ... gtgcaactagGCGTTGAAGCTTGAAGAATTTGGGGTGGAAGGCTCAGATGCTGAAAATGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaaactgctaaagttgtggccttattcttgtcacatttggctcgtgcaactagGCGTTGAAGCTTGAAGAATTTGGGGTGGAAGGCTCAGATGCTGAAAATGTTTGTTACTTACGAGATCTAGCTGATGCAAATAGGCTTGCCACTGTGATTC
tgctaaa putative branch site (score: 2)
ttattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctgaaaattgccaaaggaatttgtgctattttaaaacatagaacattaaactgctaaagttgtggccttattcttgtcacatttggctcgtgcaactagGCGTTGAAGCTTGAAGAATTTGGGGTGGAAGGCTCAGATGCTGAAAATGTTTGTTACTTACGAGATCTAGCTGATGCAAATAGGCTTGCCACTGTGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
-ctgaaaa
- - - - - - caaagga
- - - - - - - - - - - - - - - - - aaacata
- - - - - - - - - - - - - - - - - - - - - - cattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctaaagt