Sequence
atgc intronic sequence ATGC exonic sequencegttctttgtccttctgtagctagtgatgcaattatatattgttttgaaagtcttgatccttatctctcgttttggtctttctagGAAGAACTACGTCCATACTTCTCACTGCCAAAGGTTATGGATGGACTTTTCAGTCTAGCTAAGACACTTTTTGGAATTGATATTGAACCAGCAGATGGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G65620.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G65620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA01G02480.1 (Glycine max), 3'ss of exon 8
----------gttctttgtccttctgtag---ctagtgatgcaat-tatatattgttttgaaagtcttgatccttat-ctctcgttttggtctttc-tagGAAGAACTACGTCCATACTTCTCACTGCCAAAGGTTATGGATGGACTTTTCAGTCTAGCTAAGACACTTTTTGGAATTGATATTGAACCAGCAGATGGTT
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atatttttttatttttaattaatgtgtcagtctttcttttttaatgtaaacactttattggccttttaactgctcatgcttctgctgctgtatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTTAACCTTGCAAAATCACTTTTTGGCATTGAAATTGAGCCAGCTGATGGTC
upper sequence: AT5G65620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 8
-------gttctttgtccttctgtagctagtgatgcaattatatattg----ttttgaaagtcttg---atccttat-ctctcgttttggtctttc-tagGAAGAACTACGTCCATACTTCTCACTGCCAAAGGTTATGGATGGACTTTTCAGTCTAGCTAAGACACTTTTTGGAATTGATATTGAACCAGCAGATGGTT
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agattttattacttttaattaatgagtcagtctttcttttttatgttaaacacttttttggccttggaaatgctcatgcttctgctgctgtatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTTAACCTTGCAAAATCACTTTTTGGCATTGAAATTGAGCCAGCTGATGGTC
upper sequence: AT5G65620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 8
-------------gttctttgtcc-ttctgtagctagtgatgcaattatatattgttt-tgaaagtcttgatc-cttatctctcgttttggtctttc-tagGAAGAACTACGTCCATACTTCTCACTGCCAAAGGTTATGGATGGACTTTTCAGTCTAGCTAAGACACTTTTTGGAATTGATATTGAACCAGCAGATGGTT
|||||||| || | | || | | ||| | | ||| ||| || | |||| | | ||||| | |||| |||||||| || || |||||| |||||||||| |||| ||| |||||||| || ||||||| |||||||||||||| ||||| ||||| ||||||
gttgaaattgcttattctttgtgggtttttttcctgattgta-aataagccctcatttctgatagagaaacttatttattttttgttttaaaatccaacagGAGGAACTACGCCCCTATTTCTCATTGCCAAAGGTCATGGGTGGTCTTTTCAGCCTTGCTAAGATGCTTTTTGGAATTGACATTGAGCCAGCTGATGGTC
upper sequence: AT5G65620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 11
----gttctttgtccttctgtagctagtgatgcaattatatattgttttgaaagtcttgatc------cttatctctcgttttggtct----ttc--tagGAAGAACTACGTCCATACTTCTCACTGCCAAAGGTTATGGATGGAC-TTTTCAGTCTAGCTAAGACACTTTTTGGAATTGATATTGAACCAGCAGATGGTT
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aaaattcctatttctttgtgggttttttttcctgattgtaaataagcccctcatttctgatagagaaacttatttatttttttgttttaaaatccaacagGAGGAACTACGCCCCTATTTCTCATTGCCAAAGGTCATGGGTGGTCCTTTTCAGCCTTGCTAAGATGCTTTTTGGAATTGACATTGAGCCAGCTGATGGT-Mapped 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|86065054|gb|DR360811.1|DR360811EST: CCACTTTCTGGAGTGAGAGGCTTCGTGAATCCAAATACGATATTAATGAG GAAGAACTACGTCCATACTTCTCACTGCCAAAGGTTATGGATGGACTTTTC
genomic: CCACTTTCTGGAGTGAGAGGCTTCGTGAATCCAAATACGATATTAATGAGgttctttgtc ... gtctttctagGAAGAACTACGTCCATACTTCTCACTGCCAAAGGTTATGGATGGACTTTTC
EST:
gi|124915128|gb|EH989002.1|EH989002EST: CCAAATACGATATTAATGAG GAAGAACTACGTCCATACTTCTCACTGCCAAAGGTTATGGATGGACTTTTC
genomic: CCAAATACGATATTAATGAGgttctttgtc ... gtctttctagGAAGAACTACGTCCATACTTCTCACTGCCAAAGGTTATGGATGGACTTTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattatatattgttttgaaagtcttgatccttatctctcgttttggtctttctagGAAGAACTACGTCCATACTTCTCACTGCCAAAGGTTATGGATGGACTTTTCAGTCTAGCTAAGACACTTTTTGGAATTGATATTGAACCAGCAGATGGTT
tcttgat putative branch site (score: 4)
tctttct putative PPT
tatattgttttgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctttgtccttctgtagctagtgatgcaattatatattgttttgaaagtcttgatccttatctctcgttttggtctttctagGAAGAACTACGTCCATACTTCTCACTGCCAAAGGTTATGGATGGACTTTTCAGTCTAGCTAAGACACTTTTTGGAATTGATATTGAACCAGCAGATGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG