Sequence
atgc intronic sequence ATGC exonic sequence...ttagtagtaacctagtggaattaaacattttgaggtttgttccttaaatccttctacccaaagtgttaacatattttctaaatttgtcccatttctgcagATATTTTGTCTTCAAGGAAGGTTTATCTTCGGGCCGGATGTAAGATCACTTGGTCTGACCATAAGTCTTATTGTGGCACCTGTTACAATTTTCTGCATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G41060.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 1
ttagtagtaacctagtggaattaaacattttgaggtttgttccttaaatccttctacccaaagtgttaacatattttctaaatttgtcccatttctgcagATATTTTGTCTTCAAGGAAGGTTTATCTTCGGGCCGGATGTAAGATCACTTGGTCTGACCATAAGTCTTATTGTGGCACCTGTTACAATTTTCTGCATCT
|| | || || | | | | | | |||| | ||| || || |||||| ||||| ||||||||||||||| || || || || ||||| |||||||| | ||||| || | ||||||||| || |||||| || ||||||| |||
----------------------------------gtacagtttctatccatttatgactatgagggtg-cttattcattgcttttatcattttcttgcagAAATTTTTTCTTCAAGGAAGGTTCATATTTGGACCAGATGTGAGATCACTGGCGCTGACAATTATTCTTATTGTTGCTCCTGTTGCAGTTTTCTGTGTCT
upper sequence: AT5G41060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 1
ttagtagtaacctagtggaattaaacattttgaggtttgttccttaaatccttctacccaaagtgttaacatattttctaaatttgtcccatttctgcagATATTTTGTCTTCAAGGAAGGTTTATCTTCGGGCCGGATGTAAGATCACTTGGTCTGACCATAAGTCTTATTGTGGCACCTGTTACAATTTTCTGCATCT
|||| | | ||||| | || | || | | || | ||| | || | || | | | |||||||||||||| |||||| || ||| |||| || || || ||||| ||||| || || ||||||||| |||||||| || |||||||| ||||||| |||
ttagacatttaaggtttgaattcattatgtggaaatgataatgagtgttttttatttccatgctcgggacgtcaccatctgtttcattacttgtctgcagATATTTTTTCTTCAGGGGAGGCTTATATTTGGACCCGATGTTAGATCTCTGGGGCTGACCATATTCCTTATTGTTGCTCCTGTTACGGTTTTCTGTGTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatccttctacccaaagtgttaacatattttctaaatttgtcccatttctgcagATATTTTGTCTTCAAGGAAGGTTTATCTTCGGGCCGGATGTAAGATCACTTGGTCTGACCATAAGTCTTATTGTGGCACCTGTTACAATTTTCTGCATCT
ttctaaa putative branch site (score: 2)
tttgtcccatttct CT-rich tract
tgttaacatattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagtagtaacctagtggaattaaacattttgaggtttgttccttaaatccttctacccaaagtgttaacatattttctaaatttgtcccatttctgcagATATTTTGTCTTCAAGGAAGGTTTATCTTCGGGCCGGATGTAAGATCACTTGGTCTGACCATAAGTCTTATTGTGGCACCTGTTACAATTTTCTGCATCT
- - - - - - - - - - -taaacat
- - - - - - - - - - - - - - - - -ggtttgt
- - - - - - - - - - - - - - - - - - - - -ccttaaa