Sequence
atgc intronic sequence ATGC exonic sequence...ggagatcattatgcttttcttgcattaggttcttatacctctgtgataaatattactaatatgaagcaggttttggcacccgaaatgagcttggccacagTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAGTGGTCCAGTCAAGATGATTGCAACTTGAAACGAATGTTCACCCTAGGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g06810.4 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g06810.4 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA03G40440.3 (Glycine max), 3'ss of exon 17
----------------------ggagatcattatgcttt-----------tcttgcattaggttcttatacctctgtgataaatattactaatatgaagcaggttttggcacccgaaatgagcttggccacagTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAGTGGTCCAGTCAAGATGATTGCAACTTGAAACGAATGTTCACCCTAGGAG
|| | ||| | |||| | || ||||| | | | | | | | | | || ||| ||||| || | || ||||||||||| ||||||||||| |||||| | |||||||| |||| || ||| |||| || |||| | | || || || |||
tgaatgttgttttatttgattcacagttgattttactttgtatgatactatttttcattaaagtaatgtgctttta-gccagctgttcggtttatttc-cagGTGCTGTCTCCTGAAATGAGCTTAGCCACAGTGCGAGCTTATATATGGAAGAAATCAGATGACTTGGTTCTAAATTACAGACTAGTTCAAGGCAGTTGAC-------------------------------
upper sequence: LOC_Os12g06810.4 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA19G42990.1 (Glycine max), 3'ss of exon 18
-------------------------------------------------ggagatcattatgcttt-----------tcttgcattaggttcttatacctctgtgataaatattactaatatgaagcaggttttggcacccgaaatgagcttggccacagTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAGTGGTCCAGTCAAGATGATTGCAACTTGAAACGAATGTTCACCCTAGGAG
| | | | |||||| | || ||||| | | | | | | | | | || ||| |||||| || | || ||||||||||| ||||||||||| |||||| | |||||||| |||| || ||| |||| || |||| | | || || || |||
gttttttgatattgtttggcccaaattgattgaatgttttatttgattcacaattgactttgctttgtgagatactgtttttcattaaagtaatgtgcattta-gccagctgttcggtttatttc-cagGTTCTGTCTCCTGAAATGAGCTTAGCCACAGTGCGAGCTTATATATGGAAGAAATCAGATGACTTGGTTCTAAATTACAGACTAGTTCAAAGCAGGTGA--------------------------------
upper sequence: LOC_Os12g06810.4 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA19G43070.1 (Glycine max), 3'ss of exon 17
----------------------ggagatcattatgcttt-----------tcttgcattaggttcttatacctctgtgataaatattactaatatgaagcaggttttggcacccgaaatgagcttggccacagTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAGTGGTCCAGTCAAGATGATTGCAACTTGAAACGAATGTTCACCCTAGGAG
|| | ||| | |||| | || |||| | | | | | | | | | || ||| ||||| || | || ||||||||||| |||||||| || |||||||| |||||||| |||| || ||| |||| || |||| | | || || || |||
tgaatgttgttttatttgattcacagttgattttactttgtatgatactgtttttcattgaagtaatgtgctttta-gccagctgtttggtttatttc-cagGTGCTGTCTCCTGAAATGAGCTTAGCCACAGTTCGAGCTTATGTATGGAAGAAATCAGATGACTTGGTTCTAAATTACAGACTAGTTCAAGGCAGGTGA--------------------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|88906970|gb|CI376042.1|CI376042EST: AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAG TGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAG
genomic: AACCATGGCAAAAATTGAAACCTTCTGTAGAGATATTGTGTAACAGCCAGgcaagtattt ... ttggccacagTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaatattactaatatgaagcaggttttggcacccgaaatgagcttggccacagTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAGTGGTCCAGTCAAGATGATTGCAACTTGAAACGAATGTTCACCCTAGGAG
tactaat putative branch site (score: 1)
tattactaatatgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggagatcattatgcttttcttgcattaggttcttatacctctgtgataaatattactaatatgaagcaggttttggcacccgaaatgagcttggccacagTGCGGGCTTATGTCTGGAAGAAGCCAGAGGATTTGATTCTTAACTACAAAGTGGTCCAGTCAAGATGATTGCAACTTGAAACGAATGTTCACCCTAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - -tatgctt
- - - - - - - - -tcttgca
- - - - - - - - - - - - - - - - - - - - -tgtgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcaccc