Sequence
atgc intronic sequence ATGC exonic sequence...ttagattttctgactcaaggacagtattattcctatctgattaatctcatgatttgtttaattagacactatataatctgtacaaatattatgcatgcagTTGGTGATAAATTTACTCAAAATTCTTTGTACAAATGCTGCATGGCAAAGGCGTAAGCTAGGGAAAATGTTACAAGACTGGCGTGTCACCTATGTACAG
Basic information
species | Glycine max |
transcript | GLYMA17G11890.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G11890.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g55950.2 (Oryza sativa), 3'ss of exon 9
---------ttagattttctgactcaaggacagtattattcctatctgat-taatctcatgatttgtttaattagacac--tatataatctgtacaaatattatgcatgcagTTGGTGATAAATTTACTCAAAATTCTTTGTACAAATGCTGCATGGCAAAGGCGTAAGCTAGGGAAAATGTTACAAGACTGGCGTGTCACCTATGTACAG
| | | | | | | | | | ||||| || | || || | | | | || ||| | | || | | | | || ||||||| || ||||| || |||||||||||||| || ||||||||||| |||| ||||| ||||| | || || || ||| || || | |||||
gtcagccaccagaactatgcaattt--gcttaatgatttctgtatctcatgcagtcatataaaat-tatgcctaaacatgtcttttgattaagtgcattgatggccttgtagTTGGTAATCAATTTGCTTAAAATTCTTTGTACGAACACTGCATGGCAACGGCGCAAGCTTGGGAAGAGTTTGCAGGATTGGAGTACCATTTCCATACAG
upper sequence: GLYMA17G11890.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G178919_T01 (Zea mays), 3'ss of exon 1
ttagattttctgactcaaggacagtattattcct-atc--tgattaatctcatgatttgtttaattagacactatataatctgtacaaatattatg-cat-gcagTTGGTGATAAATTTACTCAAAATTCTTTGTACAAATGCTGCATGGCAAAGGCGTAAGCTAGGGAAAATGTTACAAGACTGGCGTGTCACCTATGTACAG
|| ||| | |||| | | || | | | || || ||| | | | | |||||| | || | ||| | || || ||||| ||| ||| ||||||||| || || | | ||||||||||||||||| ||||||||||| |||| ||||| ||||| | || || || ||| || | | |||||
-------gtcagacaccaggatattcttctcctttgtcagtggttattttgcttctgtgtttatctgga-attat-cactcattaataatatgatgacattgcagTTGGTTATCAACCTGATAAAAATTCTTTGTACAAACACTGCATGGCAACGGCGCAAGCTTGGGAAGAGTTTGCAGGATTGGAGTACTATTTCCATACAG
upper sequence: GLYMA17G11890.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g05910.t01 (Vitis vinifera), 3'ss of exon 3
----ttagattttctgactcaaggacagtattattcctatctgattaatctcatgatttgtttaattagacactatataatctgtacaaatattatgcatgcagTTGGTGATAAATTTACTCAAAATTCTTTGTACAAATGCTGCATGGCAAAGGCGTAAGCTAGGGAAAATGTTACAAGACTGGCGTGTCACCTATGTACAG
|| | | | | ||| | | | | | | | || ||| | ||| | | | | | ||| | || | | ||||||| ||||| ||||| || ||||| || |||||||||||||||||||||||||||||||| |||||||| |||||||| |||||||| | ||||||||||
tatgttgggtctgtgtgcagaagacgtgggaaagtacccttcttccagtttcttgagcaagatgattctaatatctgcagtttgttct----tttttcctgcagTTAGTGATCAATTTGCTTAAAATCCTGTGTACAAATGCTGCATGGCAAAGGCGTAAGCTTGGGAAAATTTTACAAGATTGGCGTGTTATCTATGTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcatgatttgtttaattagacactatataatctgtacaaatattatgcatgcagTTGGTGATAAATTTACTCAAAATTCTTTGTACAAATGCTGCATGGCAAAGGCGTAAGCTAGGGAAAATGTTACAAGACTGGCGTGTCACCTATGTACAG
gtttaat putative branch site (score: 4)
tatataatctgtacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagattttctgactcaaggacagtattattcctatctgattaatctcatgatttgtttaattagacactatataatctgtacaaatattatgcatgcagTTGGTGATAAATTTACTCAAAATTCTTTGTACAAATGCTGCATGGCAAAGGCGTAAGCTAGGGAAAATGTTACAAGACTGGCGTGTCACCTATGTACAG
- - - - -ctgactc
- - - - - - - - - - - - - - - - ctatctg
- - - - - - - - - - - - - - - - - - - - - - -ctcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgtac