Sequence
atgc intronic sequence ATGC exonic sequence...tacctgaaatgagagttacttttcatttccctccaaaaccctctgtctcaaacataggttgagagttttttaatatgtatttctcattcatttgtggcagGTAACTGACGTTGTTTTCCTGAGTTCTGGGAAAAAGCTTGTTAGTTCCTCCAAAGACAAGTTCTTGAGAGTGTGGGATATTGATACCCAGCATTGTATGC
Basic information
species | Glycine max |
transcript | GLYMA03G34360.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G34360.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G21540.1 (Arabidopsis thaliana), 3'ss of exon 2
---------tacctgaaatgagagttacttttcatttccctccaaaaccct-ctgtctcaaacataggttgagagt--tttttaatatg--tatttctcattcatttgtggcagGTAACTGACGTTGTTTTCCTGAGTTCTGGGAAAAAGCTTGTTAGTTCCTCCAAAGACAAGTTCTTGAGAGTGTGGGATATTGATACCCAGCATTGTATGC
| || ||| | || | | | | | || || | || | ||| ||||| | | | | | |||| | | | |||| || || |||| ||| || | ||| || || ||||| ||||| || || ||||||||||||||||| |||||| |||| ||||| || |||||||
gttatttaatgtctagcttgatatttctagtatttagtgtttgatgattctgctatggtgtgtgggtttttatagtggtttttgacaagagcaatgttcatgtgtctaatgtagGTCACAGATCTTGTATTCTTGGATGGTGGTAAGAAACTTGTAAGTTCATCTAAGGACAAGTTCTTGAGAGTCTGGGATCTTGAGACCCAACACTGTATGC
upper sequence: GLYMA03G34360.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g04690.t01 (Vitis vinifera), 3'ss of exon 2
--------------tacctgaaatgagagtt--acttttcatttccctcca--aaaccctctgtctcaaacataggttgagagttttttaatatg---------tatttctcattc-atttgtggcagGTAACTGACGTTGTTTTCCTGAGTTCTGGGAAAAAGCTTGTTAGTTCCTCCAAAGACAAGTTCTTGAGAGTGTGGGATATTGATACCCAGCATTGTATGC
| | || ||| | | |||| || | | | | | ||| || | | || | | | | | ||| || |||| | || | ||| | |||| || ||| |||||||| || |||||| ||||| ||||||||||| ||||||||||| || |||||||| |||||| |||| ||||| || |||||||
gtttttatttgagatttcccaatcaagatcttaaattttgatatatatatattgagcttgctgcttcttgttttg-tttataatatctaaatgtggtgagttcctattgtttgttttacatgttgtagGTCACCGACCTTGTTTTCTTGGATTCTGGTAAAAAACTTGTTAGTTCATCCAAAGACAAATTTTTGAGAGTTTGGGATCTTGAAACCCAACACTGTATGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcaaacataggttgagagttttttaatatgtatttctcattcatttgtggcagGTAACTGACGTTGTTTTCCTGAGTTCTGGGAAAAAGCTTGTTAGTTCCTCCAAAGACAAGTTCTTGAGAGTGTGGGATATTGATACCCAGCATTGTATGC
ttttaat putative branch site (score: 3)
tttctcattcattt putative PPT
ttttttaatatgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacctgaaatgagagttacttttcatttccctccaaaaccctctgtctcaaacataggttgagagttttttaatatgtatttctcattcatttgtggcagGTAACTGACGTTGTTTTCCTGAGTTCTGGGAAAAAGCTTGTTAGTTCCTCCAAAGACAAGTTCTTGAGAGTGTGGGATATTGATACCCAGCATTGTATGC
-acctgaa
- - - - - - - - - - - - - ttccctc
- - - - - - - - - - - - - - - - -caaaacc
- - - - - - - - - - - - - - - - - - - - ctctgtc
- - - - - - - - - - - - - - - - - - - - - - - - caaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttgag