Sequence
atgc intronic sequence ATGC exonic sequence...gtgcttgtttacttaaatatatcatgttactgaacttccactaatctatctgtttatacatgtatgatgatgcgttctatttccttggtttttcttttagGTTATTCCATTTGATAATAAGGGACAGCTCAAGGAAGCTTTTAATATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G05420.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 6
-----------gtgcttgtttact------taaatatatcatgttactgaacttccactaatctatctgtttata--catgtatgatgatgcgttctatttcct--tggtttttcttttagGTTATTCCATTTGATAATAAGGGACAGCTCAAGGAAGCTTTTAATATCAG
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gtatgtaacttcttctcattcactatcctgtaaaaatattagaagattaaaatgacaata-tgtttctgttcagtgtcatgttaaagtatttgaatgattcactgttcattgatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
upper sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 6
-----------gtgcttgtttact------taaatatatcatgttactgaacttccactaatctatctgtttatacatgtatgatgatgcgttctatt---tccttggtttttcttttagGTTATTCCATTTGATAATAAGGGACAGCTCAAGGAAGCTTTTAATATCAG
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gtatgtaatttcttctcattcaccatcctgtaaaaatattagaagattagaatgacaata-tgtttctgttta-atgt-catgttaaagtatttgaatgaactgttcattgatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
upper sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------gtgcttgtttacttaaatatatcatgttact--gaacttccactaatctatctg-tttatacatgtatga-----tgatgcgttctatttccttggtttttcttttagGTTATTCCATTTGATAATAAGGGACAGCTCAAGGAAGCTTTTAATATCAG
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gtatgtagtcctgactgctgattataacttttatattctatcctcctttttgtgtttttatgcctgtttgcttagagattccaataagtttttagatttactaatgctttagaatttgaagaattatcatcacaagtttgtttctttagGTGATTCCGTTTGATAATAAAGGACAGCTGAAGGAGGCGTTTAATATTAGMapped 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|116483004|gb|EG525596.1|EG525596EST: CAATGGGGGATGTTTCTGATCGTATAGGCCGGCCAACAGACAATGGTCAG GTTATTCCATTTGATAATAAGGGACAGCTCAAGGAAGCTTTTAATATCAG
genomic: CAATGGGGGATGTTTCTGATCGTATAGGCCGGCCAACAGACAATGGTCAGgtattgaata ... tttcttttagGTTATTCCATTTGATAATAAGGGACAGCTCAAGGAAGCTTTTAATATCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatctgtttatacatgtatgatgatgcgttctatttccttggtttttcttttagGTTATTCCATTTGATAATAAGGGACAGCTCAAGGAAGCTTTTAATATCAG
ttctatttccttggtt CT-rich tract
tttttctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcttgtttacttaaatatatcatgttactgaacttccactaatctatctgtttatacatgtatgatgatgcgttctatttccttggtttttcttttagGTTATTCCATTTGATAATAAGGGACAGCTCAAGGAAGCTTTTAATATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - acttaaa
- - - - - - - - - - - - - - - - - - -ccactaa
- - - - - - - - - - - - - - - - - - - - - - -ctatctg