Sequence
atgc intronic sequence ATGC exonic sequence...tagtaaaaaaaggtttaattgacttcagtgataattatctccttgagcttcgcttctctctgaatccttattactgcatgaatattctatttatgctcagGTGTTCCAAAAACGTTTGCCACCAGAAGCAGTTGATCTTCTTTGTAGGTTCTTCCAATATTCCCCCAATTTGAGATGTACAGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09840.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G09840.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA12G28730.1 (Glycine max), 3'ss of exon 10
---tagtaaaaaaaggtttaattgac--ttcagtgataattatctccttgagct-tcgcttctctctgaatccttattactgcatgaatattctatttatgctcagGTGTTCCAAAAACGTTTGCCACCAGAAGCAGTTGATCTTCTTTGTAGGTTCTTCCAATATTCCCCCAATTTGAGATGTACAGCT
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acatattggtaaaacttgtgcgtgaatgtctaacctacattatttcaaaggattcttggttgaatgtgagat----ttactgtgttatgatcctaatt-tgat-agGTCTTTCAGAAACGTTTACCCCCAGAAGCAGTGGACCTTGTCTGTAGGTTCTTTCAGTACTCCCCCAATTTGAGATGCACTGCA
upper sequence: AT1G09840.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA16G00400.2 (Glycine max), 3'ss of exon 9
tagtaaaaaaaggtttaattgacttcagtgataattatctccttgagct-tcgcttctctctgaatccttattactgcatgaatattctatttatgctcagGTGTTCCAAAAACGTTTGCCACCAGAAGCAGTTGATCTTCTTTGTAGGTTCTTCCAATATTCCCCCAATTTGAGATGTACAGCT
| |||| || | | || || | ||||| || | | | | || || ||| |||||| | || ||| || || | |||| || || |||||||| || ||||||||||| || ||| | ||||||||||| || || || |||||||||||||| || ||
--ggtaaaacttgtatgaatgtct--aacctacattatttcaaaggattcttggttgactgtgagat----ttactgtgatatgatcctaatt-tgat-aggtttttcagAAACGTTTACCCCCAGAAGCAGTGGACCTTGTCTGTAGGTTCTTTCAGTACTCTCCCAATTTGAGATGCACTGCA
upper sequence: AT1G09840.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 9
-----tagtaaaaaaaggtttaattgacttcagtgataattatctccttgagct-tcgcttctctctgaatccttattactgcatgaatattctatttatgctcagGTGTTCCAAAAACGTTTGCCACCAGAAGCAGTTGATCTTCTTTGTAGGTTCTTCCAATATTCCCCCAATTTGAGATGTACAGCT
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caaagtattggtaaaacttgtatgaatgtctaacctacattatttcaaaggattcttggttgactgtgagat----ttactgtgatatgatcctaatt-tgat-agGTTTTTCAGAAACGTTTACCCCCAGAAGCAGTGGACCTTGTCTGTAGGTTCTTTCAGTACTCTCCCAATTTGAGATGCACTGCA
upper sequence: AT1G09840.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 9
tagtaaaaaaaggtttaattgacttcagtgataattatctccttgagcttcgct------tctctctgaatccttattactgcatgaatattctatttatgc-tcagGTGTTCCAAAAACGTTTGCCACCAGAAGCAGTTGATCTTCTTTGTAGGTTCTTCCAATATTCCCCCAATTTGAGATGTACAGCT
|| | ||||| |||||| || ||||| | ||||| || | | | | | || | | |||||| || | | || ||||| |||||||||||||| || |||||||| || ||| | |||||||||| ||||| || ||||||||| || |||| ||||||
-catatgacttggttt--ttgactc--gtatcaattagcat-ttgaggttagataagatattcttttacataggagattcatcatgaac-ttattctggtgtaccagGTCTTCCAAAAACGTTTACCTCCAGAAGCTGTGGATTTAGTTTGTAGGTTTTTCCAGTACTCCCCCAATCTGCGATGCACAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcttcgcttctctctgaatccttattactgcatgaatattctatttatgctcagGTGTTCCAAAAACGTTTGCCACCAGAAGCAGTTGATCTTCTTTGTAGGTTCTTCCAATATTCCCCCAATTTGAGATGTACAGCT
ttctattt CT-rich tract
atgaatattctattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagtaaaaaaaggtttaattgacttcagtgataattatctccttgagcttcgcttctctctgaatccttattactgcatgaatattctatttatgctcagGTGTTCCAAAAACGTTTGCCACCAGAAGCAGTTGATCTTCTTTGTAGGTTCTTCCAATATTCCCCCAATTTGAGATGTACAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG