Sequence
atgc intronic sequence ATGC exonic sequencegtactgcatccttctgcagaacttctctgttctggatcgaactggttattctgatattgtcataattctgattagctccttttcttcctaatatatttcgcttgtccccatcttactacagATTGGGAACCGATCAAGTGAATTTCATCCTGACGTCAGAAGGGTAAGGAGAGAAGGCTCTTATATATACGAGGAGTTTATGGCCACCGGAGGAACTGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01310.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 7
gtactgcatccttctgcagaacttctctgttctggatcgaactggttattctgatattgtcataattctgattagctccttttcttcctaatata----------tttcgct-tgtccccatcttactacagATTGGGAACCGATCAAGTGAATTTCATCCTGACGTCAGAAGGGTAAGGAGAGAAGGCTCTTATATATACGAGGAGTTTATGGCCACCGGAGGAACTGATG
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--------------------------------gaaaccaaacaacattttctgttcttcatgtattcttatgtatttttcttgtatctggatacaaaaataaactttttgttatatttctgattaaatgtagGTTGGTAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATG
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 7
gtactgcatccttctgcagaacttctctgttctggatcgaactggttattctgatattgtcataattctgattagctccttttcttcctaatatatttcgcttgtccccatcttactacagATTGGGAACCGATCAAGTGAATTTCATCCTGACGTCAGAAGGGTAAGGAGAGAAGGCTCTTATATATACGAGGAGTTTATGGCCACCGGAGGAACTGATG
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-cactagattttt------agcttc--tattttcattgtaaatgtttgtccatacatc-ttatacttct------tccgtgtgcatacacacatataatttttat-----tattgtttcagGTTGGTAACCGCTCAAGTGAGTTCCATCCAGAGGTTAGAAGAGTGAGGCGTGAAGGCTCTTATATATATGAGGAATTTATGCCAACTGGAGGAACAGATG
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ07403 (Selaginella moellendorffii), 3'ss of exon 7
gtactgcatccttctgcagaacttctctgttctggatcgaactggttattctgatattgtcataattctgattagctccttttcttcctaatatatttcgcttgtccccatcttactacagATTGGGAACCGATCAAGTGAATTTCATCCTGACGTCAGAAGGGTAAGGAGAGAAGGCTCTTATATATACGAGGAGTTTATGGCCACCGGAGGAACTGATG
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-------------------------------------------------------------------gtgatgaagcattaagcaaaatgtaacctcttacccgatgtattaatgccgcagATTGGAAATCGTTCAAGTGAGTTTCATCCCGAGATAAGACGAGTTCGAAGAGAAGGCTCTTATATCTATGAGGAGTTTATGCCAACTGGGGGAACAGATGMapped 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|116449078|gb|EG491670.1|EG491670EST: TATACTACCCTAGCTCGGCAGGTGGAGGCATGAAAGAATTGTTTCGCAAG ATTGGGAACCGATCAAGTGAAT
genomic: TATACTACCCTAGCTCGGCAGGTGGAGGCATGAAAGAATTGTTTCGCAAGgtactgcatc ... cttactacagATTGGGAACCGATCAAGTGAAT
EST:
gi|116448301|gb|EG490893.1|EG490893EST: TATACTACCCTAGCTCGGCAGGTGGAGGCATGAAAGAATTGTTTCGCAAG ATTGGGAACCGAT
genomic: TATACTACCCTAGCTCGGCAGGTGGAGGCATGAAAGAATTGTTTCGCAAGgtactgcatc ... cttactacagATTGGGAACCGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgattagctccttttcttcctaatatatttcgcttgtccccatcttactacagATTGGGAACCGATCAAGTGAATTTCATCCTGACGTCAGAAGGGTAAGGAGAGAAGGCTCTTATATATACGAGGAGTTTATGGCCACCGGAGGAACTGATG
cttgtccccatctt CT-rich tract
ttcctaatatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgcatccttctgcagaacttctctgttctggatcgaactggttattctgatattgtcataattctgattagctccttttcttcctaatatatttcgcttgtccccatcttactacagATTGGGAACCGATCAAGTGAATTTCATCCTGACGTCAGAAGGGTAAGGAGAGAAGGCTCTTATATATACGAGGAGTTTATGGCCACCGGAGGAACTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA