Sequence
atgc intronic sequence ATGC exonic sequence...taatcagtgagctcaatatcttcctgattccttttcctcataatgattcaaatactttttgaagtgtgcctgtttcattttaattactatgatgtttcagGTAGAGGCAACAATTGAGTATATATGTCGCAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAACTGCTTGACAAAC
Basic information
species | Glycine max |
transcript | GLYMA02G35240.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G119671_T01 (Zea mays), 3'ss of exon 2
taatcagtgagctcaatatcttcctgattccttttcctcataatgattcaaatactttttgaagtgtgcctgtttc-attttaattactatgatgtttcagGTAGAGGCAACAATTGAGTATATATGTCGCAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAACTGCTTGACAAAC
| | | || || | ||| | | | || | |||| ||| | |||| | | || ||| ||| |||| || |||||||||||||| |||||| ||||||| | || ||||| ||||| || || |||||||||||||||||||| || || || |||||
tgtcacatttgtgcactagaactattatttgaacttaatacactgctaaccatacccag-gaaaaatagttgttgctaacacctctatgttgacattttagGTGGAAAGTACAATTGAGTATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA
upper sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G052798_T01 (Zea mays), 3'ss of exon 3
taatcagtgagctcaatatcttcctgattccttttcctcataatgattcaaatactttttgaagtgtgcctgtttc-attttaattactatgatgtttcagGTAGAGGCAACAATTGAGTATATATGTCGCAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAACTGCTTGACAAAC
| | | || | | ||| | | | | | |||| ||| | || | | | || ||| ||| |||| || |||||||||||||| |||||| ||||||| | || ||||| ||||| || || |||||||||| ||||||||| || || || || ||
tgtcacatttgtgcaccagaactattatttgaacttaatacactactaaccatacccag-gaaaaataattgctgctaacacctctatgttgacattttagGTGGAAAGTACAATTGAGTATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGTTGAAATTTCGAAGCTTCTAGATAAGA
upper sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 11
taatcagtgagctcaatatcttcctgattccttttcctcataatgattcaaatactttttgaagtgtgcctgtttcattttaattactatgatgtttcagGTAGAGGCAACAATTGAGTATATATGTCGCAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAACTGCTTGACAAAC
| | | || | | ||| | | | || | |||| || | | | || ||| ||| |||| || |||||||| ||||| |||||| ||||||| | || ||||| ||||| || || |||||||||||||||||||| || || || |||||
tgtcacatttgtgcaccagaactattatttgaacttaatacactgctaaccatacccaggaaaaatagttgctgctaacacctctatgttgacattttagGTGGAAAATACAATTGAATATATTTGTCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA
upper sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM5G863698_T01 (Zea mays), 3'ss of exon 4
taatcagtgagctcaatatcttcctgattccttttcctcataatgattcaaatactttttgaagtgtgcctgtttcattttaattactatgatgtttcagGTAGAGGCAACAATTGAGTATATATGTCGCAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAACTGCTTGACAAAC
| | | || | | ||| | | | || | |||| || | | | || ||| ||| |||| || |||||||||||||| |||| | ||||||| | || ||||| ||||| || || | |||||||||||||||||| || || || |||||
tgtcacatttgtgcaccagaactattatttgaacttaatacactgctaaccatacccaggaaaaatagttgctgctaacacctctatgttgacattttagGTGGAAAGTACAATTGAGTATATTTGTCACTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTATTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA
upper sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G381470_T01 (Zea mays), 3'ss of exon 8
taatcagtgagctcaatatcttcctgattccttttcctcataatgattcaaatactttttgaagtgtgcctgtttcattttaattactatgatgtttcagGTAGAGGCAACAATTGAGTATATATGTCGCAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAACTGCTTGACAAAC
| | | || | | ||| | | | || | |||| || | | | || ||| ||| |||| || |||||||||||||| | |||| ||||||| | || ||||| ||||| || || |||| ||||||||||||||| || || || |||||
tgtcacatttgtgcaccagaactattatttgaacttaatacactgctaaccatacccaggaaaaatagttactgctaacacctctatgttgacattttagGTGGAAAGTACAATTGAGTATATTTATCGCTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTACTGACTGGGATGAAATTTCGAAGCTTCTGGACAAGA
upper sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G395467_T01 (Zea mays), 3'ss of exon 3
taatcagtgagctcaatatcttcctgattccttttcctcataatgattcaaatactttttgaagtgtgcctgtttcattttaattactatgatgtttcagGTAGAGGCAACAATTGAGTATATATGTCGCAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAACTGCTTGACAAAC
| | | || | | ||| | | | || | |||| || | | | || ||| ||| |||| || |||||||||||||| |||| | ||||||| | || ||||| ||||| || || | |||||||||||||||||| || || || |||||
tgccacatttgtgcaccagaactattatttgaacttaatacactgctaaccatacccaggaaaaatagttgctgctaacacctctatgttgacattttagGTGGAAAGTACAATTGAGTATATTTGTCACTATGAAGCAGAAGGTGCAATCCTTGTGTTCCTTATTGGCTGGGATGAAATTTCGAAGCTTCTGGACAAGA
upper sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 9
taatcagtg--agctcaatatcttcctgattccttttcctcataatgattcaaatactttttgaagtgtgcctgtttcattttaattactatga---tgtttcagGTAGAGGCAACAATTGAGTATATATGTCGCAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAACTGCTTGACAAAC
|| | | | | | | |||| | || | | || || | || ||||| | | | | || | | ||| |||| |||||||||||||| |||| ||||| ||||| |||||| || |||||||| || || |||||||||||||| ||||| ||||||||||| |||
gtatgaatttcactttattctcttggtaatccagctaattccagcccatatcatcttttactgaagaat-ctcatcatgaactgatctttgaaactctgtcgtagGTGGAGGCAACAATTGAACATATTTGTCGTCTTGAAGGTGGTGGGGCGATTCTTGTCTTCCTTACTGGCTGGGATGAGATTTCAAAACTGCTTGAAAAAA
upper sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 9
taatcagtgagctcaatatcttcctgattccttttcctcataa-tgattcaaatactttttg-aagtgtgcctgtttcattttaattactatgatgttt-cagGTAGAGGCAACAATTGAGTATATATGTCGCAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAACTGCTTGACAAAC
|| | | ||| | | | | |||||| || || | |||| || || | ||| | | | || | || |||| || ||||||||||| |||| |||||| |||||| | ||||||||||||||||| ||||||||||||||||| |||||||| || |||||||||
---tctcaaatgatgacatccctaagtgcacgtcgcttcataaatgctttttcttctttatgtaattacagtaatttagatcccacttaattgttattcatagGTTGAAGCAACAATTGAACATATTTGTCGCCATGAAGGGGAAGGAGCAATTCTTGTATTCCTCACTGGCTGGGATGACATTTCTAATCTACTTGACAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcaaatactttttgaagtgtgcctgtttcattttaattactatgatgtttcagGTAGAGGCAACAATTGAGTATATATGTCGCAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAACTGCTTGACAAAC
ttttaat putative branch site (score: 3)
tttcattttaattact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taatcagtgagctcaatatcttcctgattccttttcctcataatgattcaaatactttttgaagtgtgcctgtttcattttaattactatgatgtttcagGTAGAGGCAACAATTGAGTATATATGTCGCAATGAAGCTGGTGGAGCAATTCTTGTATTTCTCACTGGCTGGGATGAAATTTCTAAACTGCTTGACAAAC
- - - - - - - - - - - - tgattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcctg