Sequence
atgc intronic sequence ATGC exonic sequence...attttctttgattttgatgttaatgttatagcttaaatacaaaataaatgtttttctaaactcttcatgtatttcttatcattttggctttgaactatagGCATAAGCTTGCACAATTTTCCAGAAGGGATGGCTGTATTTCTCGGATCAATAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G20870.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G03820.2 (Glycine max), 3'ss of exon 5
----attttctttgattttgatgttaatgttatagcttaaatacaaaataaa---tgtttttctaaactcttcatgtatttcttatcattttggctttgaactatagGCATAAGCTTGCACAATTTTCCAGAAGGGATGGCTGTATTTCTCGGATCAATAAAG
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aaaaattccttgttaattaaagacttgagc---aacttcaattctcatttttctttgtttctttgagttct----gttttttttcttcttttttgttcttttcctagGCATAAGTTTGCACAATTTTCCAGAAGGAATGGCAGTGTTCCTTGGATCCTTAAAG
upper sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G41580.5 (Glycine max), 3'ss of exon 5
--attttctttgattttgatgttaatgttatagcttaaatacaaaataaatgtttttctaaactcttcatgtatttcttatcattttggctttgaactatagGCATAAGCTTGCACAATTTTCCAGAAGGGATGGCTGTATTTCTCGGATCAATAAAG
| || |||| | | | | | | || | ||| || ||| ||| |||| || || || | |||| | | || |||||||||| |||||||||||||||||||| ||||| || || || ||||| |||||
agagttaaaaaatctttgttaattagagacttgatcaacttcaattctcatttttctctgt-ttctttgagttctttttcttttttttgttcatttct-tagGCATAAGTTTGCACAATTTTCCAGAAGGAATGGCGGTGTTCCTTGGATCCTTAAAG
upper sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 5
attttctttgattttgatgt-taatgttatagcttaaatacaaaataaatgtttttctaaactcttcatgtatttcttatcattttggctttgaactatagGCATAAGCTTGCACAATTTTCCAGAAGGGATGGCTGTATTTCTCGGATCAATAAAG
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ctttgagtcgcttttgtggcatctctttataaatgaatttttctttacttatcaaaaaaaaaaaaaaaattaacagggaaccttatc-ctctgagttgcagGCATAAGCTTGCACAATTTTCCCGAGGGAATGGCTGTGTTCCTTGGATCAATGAAGMapped 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|116403230|gb|EG445822.1|EG445822EST: GAAGAAGCATCGCCAGCAAGTCTTATATAATGGACTTATAACAGCTATAG GCATAAGCTTGCACAATTTTCCAGAAGGGATGGCTGTATTTCTCGG
genomic: GAAGAAGCATCGCAAGCAAGTCTTATATAGTGGACTTATAACAGCTATAGgtatactaac ... tgaactatagGCATAAGCTTGCACAATTTTCCAGAAGGGATGGCTGTATTTCTCGG
EST:
gi|124990618|gb|EL062887.1|EL062887EST: GAAGAAGCATCGCAAGCAAGTCTTATATAGTGGACTTATAACAGCTATAG GCATAAGCTTGCACAATTTTCCAGAAGGGATGGCTGTATTTCTCGGA
genomic: GAAGAAGCATCGCAAGCAAGTCTTATATAGTGGACTTATAACAGCTATAGgtatactaac ... tgaactatagGCATAAGCTTGCACAATTTTCCAGAAGGGATGGCTGTATTTCTCGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgtttttctaaactcttcatgtatttcttatcattttggctttgaactatagGCATAAGCTTGCACAATTTTCCAGAAGGGATGGCTGTATTTCTCGGATCAATAAAG
ttctaaa putative branch site (score: 2)
tatttcttatcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttctttgattttgatgttaatgttatagcttaaatacaaaataaatgtttttctaaactcttcatgtatttcttatcattttggctttgaactatagGCATAAGCTTGCACAATTTTCCAGAAGGGATGGCTGTATTTCTCGGATCAATAAAG
- - - - -gattttg
- - - - - - - - - - - - - - - - - aaataca
- - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaact