Sequence
atgc intronic sequence ATGC exonic sequence...aactgtaccatcgctttcaaaatgtttaagttttcaagtttctgtatttctgtttaaatgtttcagcattttgacatttgagacctgtgtcaattttcagATAAACCCGCAATTCTATGCATTCAGATGGATCACACTCCTATTGACTCAAGAATTCAATTTCGTGGAAAGCCTTCACATCTGGGACACACTCTTAAGCG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G13730.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G11760.1 (Glycine max), 3'ss of exon 7
aactgtaccatcgctttcaaaatgtttaagttttcaagtttctgtatttc-tgtttaaatgtttcagcattttgacatttgagacctgtgtcaattttcagATAAACCCGCAATTCTATGCATTCAGATGGATCACACTCCTATTGACTCAAGAATTCAATTTCGTGGAAAGCCTTCACATCTGGGACACACTCTTAAGCG
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-tttgcgtgcacacctgctggatgattcaaccaatgtatttttgcttttggttattgaacagtttatcagatgggtcatgttttctggttctgaatgtcagGTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAGGAATTCAATTTTGCTGACAGCCTTCACATTTGGGACACTCTTTTAAGCG
upper sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 7
--aactgtaccatcgctttcaaaatgtttaagttttcaagtttctgtatttctgtttaaatgtt--tcagcattttgacatttgagacctgtgtcaattttcagATAAACCCGCAATTCTATGCATTCAGATGGATCACACTCCTATTGACTCAAGAATTCAATTTCGTGGAAAGCCTTCACATCTGGGACACACTCTTAAGCG
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ttttttgcatgcacacctgctggatgattcaaccatgtatttgcttt-tggctattgaacagtttatcagattgctcatatttt---ctggttctgaatttcagGTCAATCCTCAATTCTATGCATTTAGGTGGATTACTCTCCTGCTGACTCAGGAATTCAATTTTGCCGACAGCCTTCACATTTGGGATACTCTTTTAAGCG
upper sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 7
aactgtaccatcgctttcaaaatgtttaagtttt--caagtttctgtatttctgt--ttaaatgtttcagcattttgacatttgagac-ctgtgt---caattttcagATAAACCCGCAATTCTATGCATTCAGATGGATCACACTCCTATTGACTCAAGAATTCAATTTCGTGGAAAGCCTTCACATCTGGGACACACTCTTAAGCG
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--------cataagctggcagatgtttggacttcagtgaattacatcatttttacccttggttggtcaatctctcagatgtctgatgctctatatttgcaaatggcagGTCAATCCCCAATTTTATGCATTTAGATGGATAACTCTCCTCTTGACTCAAGAGTTCAATTTTGCGGACAGCCTTCACATTTGGGACACACTTCTAAGTGMapped 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|116409994|gb|EG452586.1|EG452586EST: TGAAGCATCATGATGAAGAACTTTGGCGTCATTTAGAAGTCACAACCAAA ATAAACCCGCAATTCTATGCATTCAGATGGATCACACTCCTATTGACTCAA
genomic: TGAAGCATCATGATGAAGAACTTTGGCGTCATTTAGAAGTCACAACCAAAgtaagatatt ... caattttcagATAAACCCGCAATTCTATGCATTCAGATGGATCACACTCCTATTGACTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttctgtttaaatgtttcagcattttgacatttgagacctgtgtcaattttcagATAAACCCGCAATTCTATGCATTCAGATGGATCACACTCCTATTGACTCAAGAATTCAATTTCGTGGAAAGCCTTCACATCTGGGACACACTCTTAAGCG
ttttgac putative branch site (score: 3)
ttttc putative PPT
tttaaatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aactgtaccatcgctttcaaaatgtttaagttttcaagtttctgtatttctgtttaaatgtttcagcattttgacatttgagacctgtgtcaattttcagATAAACCCGCAATTCTATGCATTCAGATGGATCACACTCCTATTGACTCAAGAATTCAATTTCGTGGAAAGCCTTCACATCTGGGACACACTCTTAAGCG
- - - - - - - -ttcaaaa