Sequence
atgc intronic sequence ATGC exonic sequence...tggccatttgccacttactgtttatcgctgtttttttttttggtttgtagctataactttcattatttttggagttaattaactccttttttgtgtgtagGGGATAAAAGAAGGCTGGTATGATGGAGCAAGCATTGCTTTTGCTGTTCTCCTAGTTGTTGTTGTTACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g51610.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G391042_T02 (Zea mays), 3'ss of exon 6
-------tggccatttgccactta--ctgtttatcgctgtttttttttttggtttgtagctataactttcattatttttggagttaattaactccttttttgtgtgtagGGGATAAAAGAAGGCTGGTATGATGGAGCAAGCATTGCTTTTGCTGTTCTCCTAGTTGTTGTTGTTACAG
| ||| | || | |||| | | | | || ||||| | || | | | |||||||| | | | || | || ||||| |||||||||||||||||||||||||| |||||||| ||||||||||| |||||||| |||||||||
gcagatttcatcatattcccttgcatctgtatgtgcttactgcttccattggtgctcatctgtg--ctcctttatttttacattggaata-------tgatgacattagGGCATAAAAGAAGGCTGGTATGATGGAGCGAGCATTGCCTTTGCTGTTCTTCTAGTTGTATTTGTTACAG
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 6
tggccatttgccacttactgt-ttatcgctgtttttttttttggtttgtagctataactt-tcattatttttggagttaattaactccttttttgtgtgtagGGGATAAAAGAAGGCTGGTATGATGGAGCAAGCATTGCTTTTGCTGTTCTCCTAGTTGTTGTTGTTACAG
|| || | | || || |||| || | | | || ||| || || || | || | | || | | || ||||| |||||||||||||||||||||||||| |||||||| ||||||||||| |||||||| |||||||||
--gcagatttcatcatattgccttatatctttccatgtgcttacattgattacattgctcatctgtgttcctttattttgcattggaatatgatgatattagGGCATAAAAGAAGGCTGGTATGATGGAGCGAGCATTGCCTTTGCTGTTCTTCTAGTTGTATTTGTTACAG
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 5
tggccatttgccacttactgtttatcgctgtttttttttttggtttgtagctataactttcattatttttggagttaattaactcc----ttttttgtgtgt-agGGGATAAAAGAAGGCTGGTATGATGGAGCAAGCATTGCTTTTGCTGTTCTCCTAGTTGTTGTTGTTACAG
||| | | | || | | | | || || | || | | | || | ||| || || | | || || ||| | |||| | || ||||| ||||||||||| | ||||||||||||||| ||| | || ||| || |||||||||
----tgcatgctagacagttttccttcataatctgggattaggaata-agtttttgttgatgctaggaattaggtttatcaagttcagacttaattatgtttcagGGTCTTAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATTCTTGTTATTCTTGTTACAG
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 5
tggccatttgccacttact-gtttatcgctgtttttttttttggttt-gtagctataactttcattatttttggagttaattaactccttttttgtgtgtagGGGATAAAAGAAGGCTGGTATGATGGAGCAAGCATTGCTTTTGCTGTTCTCCTAGTTGTTGTTGTTACAG
|| || | | || | | ||| | || | | ||| || ||| | ||||||| | || || |||||| || |||| || || ||||| ||||||||||| | ||||||||||||||| ||| | || ||| ||||||||||||
tgatgtttgatcgttctcttgataatctaggattaagagtatatttttgtgaatattgagatttttattttcatt-ctgtttgacaataattttgt-tgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATTCTTGTTATTGTTGTTACAG
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 8
tggccatttgccacttactgtttatcgctgtttttttttttggtttgtagctataactttcattatttttggag-----ttaattaactccttttttgtgtgtagGGGATAAAAGAAGGCTGGTATGATGGAGCAAGCATTGCTTTTGCTGTTCTCCTAGTTGTTGTTGTTACAG
||| | || || ||||| | ||||| ||| || | | | || ||| | || | || | | ||| | | ||||| | ||||| ||||||||||| | ||||||||||||||| ||||| || || |||| |||||||
--attattc-ttgccagttgaataa-attgtttggtattttgtattg-agttgacaaagttatcattctcaaaggtttatcctttcatttatttctaattgatagGGTTTGGCTGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTCTTCTTGTCATTGTAGTTACAG
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G00630.1 (Glycine max), 3'ss of exon 8
tggccatttgccacttactgtttatcgctgtttttttttttggtttgtagctataactttcattatttttggagttaattaactccttt-tttgtgt---gtagGGGATAAAAGAAGGCTGGTATGATGGAGCAAGCATTGCTTTTGCTGTTCTCCTAGTTGTTGTTGTTACAG
|| ||| | || ||||| | |||| ||| || | | |||| | | ||| || |||||| ||||| ||||| | ||||| ||||||||||| | ||||||||||||||| ||||| || || |||| ||||| |
tgattattc-ttgtcagttaaataaatttgtttggtattttctattg-agttgacaaagtcat--tctcaaaggtttatcctttcctttatttgtaattgatagGGTTTGGCTGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTCTTCTTGTCATTGTAGTTACTG
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 5
-------tggccatttgccacttactgtttatcgctgtttttttttttggtttgtagctataactttcattatttttggagttaattaactccttttttgtgtgtagGGGATAAAAGAAGGCTGGTATGATGGAGCAAGCATTGCTTTTGCTGTTCTCCTAGTTGTTGTTGTTACAG
||| | || | | | | || | | | | ||| | | | | | ||| ||| | || || | | |||||| || |||| || || ||||| ||||||||||| | ||||||||||||||| ||| | || ||| ||||||||||||
ttatgtttggtcgtt--ctcttgataatctaggattaatcgtatatttttgtgattgttgagatttttattttcattcagtttgacga----taattttgt-tgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATTCTTGTTATTGTTGTTACAG
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 7
-----tggccatttgccacttactgtttatcgctgtttttttttttggtttgtagctataactttca--ttatttttggagttaattaactcctttt--------------ttgtgtgtagGGGATAAAAGAAGGCTGGTATGATGGAGCAAGCATTGCTTTTGCTGTTCTCCTAGTTGTTGTTGTTACAG
|| | | | | | ||| | | ||| || | ||| | | || | || ||| |||| ||| || | | | | |||| || |||||||| ||||||||||||| ||||||||| |||||||| | || || ||||||| || |
gtttgtgatgaaat-caattaactaaatttggctcttccctctttccccagagtaatgtcacctccaaattaaccttggtcttacacaatctttactaacttggataacaatcatcgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtagctataactttcattatttttggagttaattaactccttttttgtgtgtagGGGATAAAAGAAGGCTGGTATGATGGAGCAAGCATTGCTTTTGCTGTTCTCCTAGTTGTTGTTGTTACAG
aattaac putative branch site (score: 2)
ttaactcctttttt CT-rich tract
attatttttggagtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggccatttgccacttactgtttatcgctgtttttttttttggtttgtagctataactttcattatttttggagttaattaactccttttttgtgtgtagGGGATAAAAGAAGGCTGGTATGATGGAGCAAGCATTGCTTTTGCTGTTCTCCTAGTTGTTGTTGTTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT