Sequence
atgc intronic sequence ATGC exonic sequence...ggtagagaacatacaaactgaaaaaagaaaaagaaagttgatgttttaaacgagtcattatataatctcttcttatacacgtcgattttcaattaatcagGCAAAGAGGGCTGGTTCAAAGCTGAAAAGCCGCATTGTTGCTGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
Basic information
species | Glycine max |
transcript | GLYMA09G15220.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G15220.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 3'ss of exon 12
ggtagagaacatacaa-actgaaaaaagaaaaagaaagttgatgttttaaacgagtcatta--tataatctcttcttatacacgtcgattttcaattaatcagGCAAAGAGGGCTGGTTCAAAGCTGAAAAGCCGCATTGTTGCTGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
|| | | || | || | | | | || | || |||| || || | | | || | ||||| | || ||||||||||| ||||||||| |||||||||| ||||||||||| ||| | || | | |||| | | | |||||| || | ||||| |||||||||
--taatgtatgagcattattgtgactatgatgatcaatgttat-ttttcgtttagccactgcttttgattgttacttattggtattcgttgaattgctttcagGCAAAGAAAGCTGGTTCACAGCTGAAAAGTCGCATTGTTGCAGAGAAGCCTGTGGCTGAGTGTGCAAAATTGATTGAGGAACTTGAAGATCAAATTTCTA
upper sequence: GLYMA09G15220.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G420865_T01 (Zea mays), 3'ss of exon 12
ggtagagaacatacaaactgaaaaaagaaaaagaaagttgatgttttaaacgagtcattatataatctcttcttatacacgtcgattttca-attaatcagGCAAAGAGGGCTGGTTCAAAGCTGAAAAGCCGCATTGTTGCTGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
| | || | | | | | | | | | | ||| | | ||||| | || | | ||||||||||| |||||||||| |||||||||| ||||||||||| ||| || || | | |||| | | | ||||||||| | |||| ||||||||||
-tttgtttttatcctttccctagaccctactcatgtggagcttccgacactgggtctgctctcggttgttgcttattggttttatttggcttacctttcagGCAAAGAAGGCTGGTTCACAGCTGAAAAGTCGCATTGTTGCAGAGAAACCTGTGGCTGAGTGTGCACGACTGATTGAGCAACTAGAAGGCCAAATTTCTA
upper sequence: GLYMA09G15220.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G804064_T01 (Zea mays), 3'ss of exon 12
ggtagagaacataca-aactgaaaaaagaaaaagaaagttgatgttttaaacgagtcattatataatctctt-cttatacacgtcgattt-tcaattaatcagGCAAAGAGGGCTGGTTCAAAGCTGAAAAGCCGCATTGTTGCTGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
||| || | || | || | || | ||||| | | | | || ||||| | | || | | ||||||||||| |||||||||| | |||||||||||||||||||| ||| || || | | |||| | || | ||||||||| | ||||| || |||||
--caga-aatacactcatctattgatctgtcgagctcttctgagttttggtgtttttttggcctgggttgttgcttattcgttttatttgacctacctttcagGCAAAGAAGGCTGGTTCACAACTGAAAAGCCGCATTGTTGCAGAGAAACCTGTGGCTGAGTGTGCACAACTGATTGAGCAACTAGAAGATCAGATTTCCA
upper sequence: GLYMA09G15220.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 12
ggtagagaacatacaaactgaaaaaagaaaaagaaagttgatgtttt-aaacgagtcattatataatctcttcttatacacgtcgattt--tcaattaatcagGCAAAGAGGGCTGGTTCAAAGCTGAAAAGCCGCATTGTTGCTGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
| | | || ||| |||| ||| |||| | || | | | | | | | ||| || || | |||| ||||| |||||||||||||||| ||||| |||||||| |||||||||||| ||||||||||||||| ||||| ||||||||||| ||| || |||
--tggtgttaatg-aaattgaactgggaacctcctccaccccacccccaaaccccttgccatttgaggcaggcctcaagagcttcctttaatcgatgtaacagGTGAAGAGAGCTGGTTCAAAGCTGAGGAGCCGAATTGTTGCAGAGCAATCTATAATTAAGTGGTCTCATATGATTGAACAAATGGAAGATCAAGTTGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaacgagtcattatataatctcttcttatacacgtcgattttcaattaatcagGCAAAGAGGGCTGGTTCAAAGCTGAAAAGCCGCATTGTTGCTGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
attatataatctcttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtagagaacatacaaactgaaaaaagaaaaagaaagttgatgttttaaacgagtcattatataatctcttcttatacacgtcgattttcaattaatcagGCAAAGAGGGCTGGTTCAAAGCTGAAAAGCCGCATTGTTGCTGAGCAATCTATACATAAGTGGTCTCATATAATTGAGCAAATGGAAGACCAAATTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - acataca
- - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - gttgatg