Sequence
atgc intronic sequence ATGC exonic sequence...attgtggtattagtagccatagcacttgattaggtttaggctttatcagtgtaacactcgtttcttagatctagtgtaaaagatatgtctttgttaacagGAAGAGAGAGATGCAATCTTGGCAAAGATTGAAGTTTCACAAGCACATTTAGAGTTATTAAATAAGACAAATGTACTTATTGATGCCTTCCCCATACGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61710.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61710.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 5
attgtggtattagtagccatagcacttgatt-aggtttaggctttatcagtgtaacactcgtttcttagatctag---tgtaaaagatatgtctttgttaacagGAAGAGAGAGATGCAATCTTGGCAAAGATTGAAGTTTCACAAGCACATTTAGAGTTATTAAATAAGACAAATGTACTTATTGATGCCTTCCCCATACGGA
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--tgtggc--tagaagttcaaacatgtagccgaaaattttctcctttttctgaaaaatataacttccaagtctaagcatttagcaaaaatactttaattaacagGAGGAGAGAGATGCAATTTTGGCCAAGATTGAAGTTTCACAAGCACATTTAGAATTATTGAAGCGTACAAATGTGCTCAATGATGCCTTCCCCATTTCTC
upper sequence: AT3G61710.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 5
attgtggtattagtagccatagcacttgattaggtttaggctttatcagtgtaacactcgtttcttagatctagtgtaaaagatatgtctttgttaacagGAAGAGAGAGATGCAATCTTGGCAAAGATTGAAGTTTCACAAGCACATTTAGAGTTATTAAATAAGACAAATGTACTTATTGATGCCTTCCCCATACGGA
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---------------------gtattagaa-aactttctcctttttctgaaaaata-----taataacttccagcaaaaa-----tactttaattaacagGAGGAGAGAGATGCAATTTTGGCCAAGATTGAAGTTTCACAGGCACATTTAGAATTATTGAAGCGTACAAATGTGCTCAATGACGCCTTCCCCATTTCTC
upper sequence: AT3G61710.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 5
attgtggtattagtagccatagcact-tgattaggtttag--gctttatcagtgtaacactcgtttcttagatctagtgtaaaagatatgtctttgttaacagGAAGAGAGAGATGCAATCTTGGCAAAGATTGAAGTTTCACAAGCACATTTAGAGTTATTAAATAAGACAAATGTACTTATTGATGCCTTCCCCATACGGA
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-gtatgttgctggtatataaaccgttgctgctctttttagtagttttactgctttgtctatgaatctttcaattgtttacaaagagt---tttctgtcaacagGAAGAGAGAGATGCAATTCTGGCCAAGATTGAAGTGTCACAGGCACATCTAGAGTTGTTGAAGAGAACTAATGTACTGAATGATGCCTTCCCCATTTGGCMapped 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|116473301|gb|EG515893.1|EG515893EST: GTATTGGCAAGAGTTCAATAATTTTCAGTTTCAATTAATTGCCCATCAG GAAGAGAGAGATGCAATCTTGGCAAAGATTGAAGTTTCACAAGCACATTTA
genomic: GTATTGGCAAGAGTTCAATAATTTTCAGTTTCAATTAATTGCCCATCAGgtgcgtttct ... ttgttaacagGAAGAGAGAGATGCAATCTTGGCAAAGATTGAAGTTTCACAAGCACATTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagtgtaacactcgtttcttagatctagtgtaaaagatatgtctttgttaacagGAAGAGAGAGATGCAATCTTGGCAAAGATTGAAGTTTCACAAGCACATTTAGAGTTATTAAATAAGACAAATGTACTTATTGATGCCTTCCCCATACGGA
gtgtaac putative branch site (score: 3)
tctttgtt putative PPT
taaaagatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgtggtattagtagccatagcacttgattaggtttaggctttatcagtgtaacactcgtttcttagatctagtgtaaaagatatgtctttgttaacagGAAGAGAGAGATGCAATCTTGGCAAAGATTGAAGTTTCACAAGCACATTTAGAGTTATTAAATAAGACAAATGTACTTATTGATGCCTTCCCCATACGGA
- - - - - - - - ccatagc
- - - - - - - - - - - - - - - - ggtttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaag