Sequence
atgc intronic sequence ATGC exonic sequence...caaacatctgctaaataagcatggactttaataagaacatataggtttttcttgatttgaactgtcgacttgtattgattcttgaatttgggaaatgcagATGGGCTCACATTGCAAGCCACTTGCCTGGTCGAACTGACAATGAAATAAAGAACTATTGGAACTCATGGATAAAAAAGAAGATAAGAAAGACTTCGGTG
Basic information
species | Glycine max |
transcript | GLYMA05G37460.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G37460.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G325907_T01 (Zea mays), 3'ss of exon 2
--caaacatctgctaaataagcatggactttaataagaacatataggtttttcttgatttgaac-tgtcgacttgtattgattcttgaatttgggaaatgcagATGGGCTCACATTGCAAGCCACTTGCCTGGTCGAACTGACAATGAAATAAAGAACTATTGGAACTCATGGATAAAAAAGAAGATAAGAAAGACTTCGGTG
||| ||||||| | ||| | || | | | ||||| || || || | || || | | || ||||| ||||| |||||||| ||||||||||| || || || ||||| || || |||||||| |||||||| ||||| || |||||||| | ||| | || ||
tgaaaatgaaggctaaatccaaa-ggaatgcaacacctaggctagctagctagttgatgtgtacatgaccacagccat--gtcccccggttctctctctgcagGTGGGCCCACATTGCCAGCCACTTGCCCGGGCGGACGGACAACGAGATCAAGAACTACTGGAACTCGTGGATCAAGAAGAAGATCCGGAAGCCGGCGATG
upper sequence: GLYMA05G37460.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g00320.t01 (Vitis vinifera), 3'ss of exon 2
-----caaacatctgctaaataagcatggactttaataagaacatataggtttttcttgatttgaactgtcgacttgtattgattcttgaatttgggaaatgcagATGGGCTCACATTGCAAGCCACTTGCCTGGTCGAACTGACAATGAAATAAAGAACTATTGGAACTCATGGATAAAAAAGAAGATAAGAAAGACTTCGGTG
|| || | ||| || | || | || | | | ||| ||| | || | | ||| ||| |||||||| || ||||||||||| |||||||| ||||||||||| |||| |||||||| |||||||| || ||||| || ||||| |||||||||||||| ||| | ||||
ttcgtgaagttacttccaaac--ccaccgtattcatgaactaatcacaaactttgaggtgtttcagtcttct-taaggactgacatttg--tttgggaattgtagATGGGCTCATATTGCAAGTCACTTGCCTGGAAGAACAGACAATGAGATAAAGAATTACTGGAATTCGTGGATCAAAAAGAAGATAAGGAAGCCGTCGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttcttgatttgaactgtcgacttgtattgattcttgaatttgggaaatgcagATGGGCTCACATTGCAAGCCACTTGCCTGGTCGAACTGACAATGAAATAAAGAACTATTGGAACTCATGGATAAAAAAGAAGATAAGAAAGACTTCGGTG
tattgat putative branch site (score: 3)
tattgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaacatctgctaaataagcatggactttaataagaacatataggtttttcttgatttgaactgtcgacttgtattgattcttgaatttgggaaatgcagATGGGCTCACATTGCAAGCCACTTGCCTGGTCGAACTGACAATGAAATAAAGAACTATTGGAACTCATGGATAAAAAAGAAGATAAGAAAGACTTCGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
caaacat
- - - -ctgctaa
- - - - - - - - - gcatgga
- - - - - - - - - - - - - - -aataagaa