Sequence
atgc intronic sequence ATGC exonic sequence...ttgttatgcataattttgtgtatgtttgcgagtatattcttttgttctgtgtattgatctatggcttgaattgtgtgtttgtgcatgtggagattggaagGATCCCAGAGGGCTGGAGAGGTGACCTGAGTTGCATGGGGAGAGGATGCCAGAGCTGCGAAGCAGTACTCGCCAAGCACGTCTGAGGTCTAGGAAGCCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g07560.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 1
----------ttgttatgcataattttgtgtatgtttgcgagtatattcttt--tgttctgtgtattgatctatggcttgaattgtgtgtttgtgcatgtggagattggaagGATCCCAGAGGGCTGGAGAGGTGACCTGAGTTGCATGGGGAGAGGATGCCAGAGCTGCGAAGCAGTACTCGCCAAGCACGTCTGAGGTCTAGGAAGCCTG
||| || | || ||| | || || ||| || || ||| | || |||| | | | || ||||| ||||||||||||||||||||| | | ||||||||| | | ||||||||||| |||| ||||||||||||||||||||||||||||||||||||||| | || ||||| |
tatggataggttgctagagtgagattgatgtgtattctttgccatgttcgttgctgctctttatactgatgaacgattgtaactgtgtc----tgcatgtggagATTGGAAGGAGCTCGGAGGGCTGGGGCGCTGACCTGAGTTTTATGGAGAGAGGATGCCAGAGCTGCGAAGCAGTACTCGCCAAGCATGCCTAAGGTCGAA--------
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 1
----------ttgttatgcataattttg---tgtatgtttgcgagtatattcttttgttctgtgtattgatctatggcttgaattgtgtgtttgtgcatgtggagattggaagGATCCCAGAGGGCTGGAGAGGTGACCTGAGTTGCATGGGGAGAGGATGCCAGAGCTGCGAAGCAGTACTCGCCAAGCACGTCTGAGGTCTAGGAAGCCTG
||| | | | ||||| ||||| || ||||| | ||||||| | || |||| ||| | || ||||| ||||||||||||||||||||| | | || |||||| | ||||| || || |||||||||||||||||||||||||||||| |||||| |||||||| | |||||||
gatggagaggttgctg-gagtggttttgatgtgtattctttgcagtatttgacgttgttctttatactgattaatgattgtaactgtgtc----tgcatgtggagATTGGAAGGAGCTCGGAAGGCTGGGACGCTGACCCGAATTTTATGGGGAGAGGATGCCAGAGCTGCGAAGCAATACTCGTCAAGCACGCTTAAGGTCTAA--------
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G164265_T01 (Zea mays), 3'ss of exon 1
--ttgttatgcataattttgtgtatgtttgcgagtatattcttt--tgttctgtgtattgatctatggcttgaattgtgtgtttgtgcatgtggagattggaagGATCCCAGAGGGCTGGAGAGGTGACCTGAGTTGCATGGGGAGAGGATGCCAGAGCTGCGAAGCAGTACTCGCCAAGCACGTCTGAGGTCTAGGAAGCCTG
||| || | || ||| | || || ||| || || ||| | || |||| | | | || ||||| ||||||||||||||||||||| | | ||||||||| | | ||||||||||| |||| ||||||||||||||||||||||||||||||||||||||| | || ||||| | ||||| ||
ggttgctagagtgagattgatgtgtattctttgccatgttcgttgctgctctttatactgatgaacgattgtaactgtgtc----tgcatgtggagattggaagGAGCTCGGAGGGCTGGGGCGCTGACCTGAGTTTTATGGAGAGAGGATGCCAGAGCTGCGAAGCAGTACTCGCCAAGCATGCCTAAGGTCGAAGAAGCTTG
upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G037923_T03 (Zea mays), 3'ss of exon 1
--ttgttatgcataattttg---tgtatgtttgcgagtatattcttttgttctgtgtattgatctatggcttgaattgtgtgtttgtgcatgtggagattggaagGATCCCAGAGGGCTGGAGAGGTGACCTGAGTTGCATGGGGAGAGGATGCCAGAGCTGCGAAGCAGTACTCGCCAAGCACGTCTGAGGTCTAGGAAGCCTG
||| | | | ||||| ||||| || ||||| | ||||||| | || |||| ||| | || ||||| ||||||||||||||||||||| | | || |||||| | ||||| || || |||||||||||||||||||||||||||||| |||||| |||||||| | ||||||| ||||| ||
ggttgctg-gagtggttttgatgtgtattctttgcagtatttgacgttgttctttatactgattaatgattgtaactgtgtc----tgcatgtggagattggaagGAGCTCGGAAGGCTGGGACGCTGACCCGAATTTTATGGGGAGAGGATGCCAGAGCTGCGAAGCAATACTCGTCAAGCACGCTTAAGGTCTAAGAAGCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtgtattgatctatggcttgaattgtgtgtttgtgcatgtggagattggaagGATCCCAGAGGGCTGGAGAGGTGACCTGAGTTGCATGGGGAGAGGATGCCAGAGCTGCGAAGCAGTACTCGCCAAGCACGTCTGAGGTCTAGGAAGCCTG
tattgat putative branch site (score: 3)
tattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttatgcataattttgtgtatgtttgcgagtatattcttttgttctgtgtattgatctatggcttgaattgtgtgtttgtgcatgtggagattggaagGATCCCAGAGGGCTGGAGAGGTGACCTGAGTTGCATGGGGAGAGGATGCCAGAGCTGCGAAGCAGTACTCGCCAAGCACGTCTGAGGTCTAGGAAGCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- -ttatgca
- - - - - - - - -gtgtatg
- - - - - - - - - - - - - - - - - - - - - - - - -tgtattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgt