Sequence
atgc intronic sequence ATGC exonic sequence...ttcaacagttctttttttaaatatgtttgtacaaaataaactgtttgttaattccaatatcatccttgatcttgtgtctgttttgaaaattgaaatgcagGACGCTGCCGCTTGGCTTGAATACTTTGAATCAAAAGTTATCGAGCAACAGGAAGCTGCACGCAATGGAACTCGGAAACCTGATGCATCAATTGCTAGTA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g23990.2 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 21
-----ttcaacagttctttttttaaatatgtttgtacaaaataaactgtttgttaattccaatatcatccttgatct-tgtgtctgttttgaaaattgaaatgcagGACGCTGCCGCTTGGCTTGAATACTTTGAATCAAAAGTTATCGAGCAACAGGAAGCTGCACGCAATGGAACTCGGAAACCTGATGCATCAATTGCTAGTA
| | |||| ||| | | ||| | |||| ||| | |||| || | | | |||| | | | |||| | |||| | ||||| ||||| ||||||||||| || ||||| || || | | | || || || |||||||| || ||||| ||||| ||||||||||||||||| ||||| |
attggtgctccagtctcaattt---gtctttttctttaaaaaaaatgaatgaggaattataactgtttgcataatctatagttttttttttataatttga---cagGATGCTGCGGCTTGGCTTGAGTATTTTGAGTCCAAGGCTTTTGAACAGCAAGAAGCTGCTCGAAATGGTACTCGAAAACCTGATGCATCAATAGCTAGCA
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 21
ttcaacagttctttttttaaatatgtttgtacaaaataa--actgtttgttaattccaatatcatccttgatcttgtgtctgttttgaaaattgaaatgcagGACGCTGCCGCTTGGCTTGAATACTTTGAATCAAAAGTTATCGAGCAACAGGAAGCTGCACGCAATGGAACTCGGAAACCTGATGCATCAATTGCTAGTA
|||| ||||||| | || | | | ||| | |||||||| | || | | | || | | | | |||| | || | |||||| ||||| ||||||||||| || |||||||| || | | | || || || |||||||| || ||||| ||||| ||||||||||||||||| || || |
ctcaatttgtctttttcttaaaaaaatgatgaggaattataactgtttgcataatctatagttttttttatttatttacttttttttataaatttg--gcagGATGCTGCGGCTTGGCTTGAGTATTTTGAATCCAAGGCTTTTGAACAGCAAGAAGCTGCTCGAAATGGTACTCGAAAACCTGATGCATCAATAGCCAGCA
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 21
ttcaacagttctttttttaaatatgtttgtacaaaataaactgtttg--ttaattccaatatcatc-cttgatcttgtgtctgttttgaaaattgaaatgc---agGACGCTGCCGCTTGGCTTGAATACTTTGAATCAAAAGTTATCGAGCAACAGGAAGCTGCACGCAATGGAACTCGGAAACCTGATGCATCAATTGCTAGTA
| ||||| || | || || | | ||| | |||| | | | || |||| || ||| || | || ||||| |||| ||||| |||||||| || |||||||| ||||| | | | || || || ||||||||| | ||||| ||||| |||||||||||||| || || || |
------atcatctttttgaagcacgtgtgatgattctttttaatttcattctattcaagttttgtcatttgaaagtggttctaagttctgtaatggaatgctgtagGATGCTGCTGCTTGGCTCGAGTACTTTGAGTCAAAGGCTTTTGAACAGCAAGAAGCTGCAAGAAATGGGACTCGAAAACCTGATGCATCCATAGCCAGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttaattccaatatcatccttgatcttgtgtctgttttgaaaattgaaatgcagGACGCTGCCGCTTGGCTTGAATACTTTGAATCAAAAGTTATCGAGCAACAGGAAGCTGCACGCAATGGAACTCGGAAACCTGATGCATCAATTGCTAGTA
ttttgaaaattgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaacagttctttttttaaatatgtttgtacaaaataaactgtttgttaattccaatatcatccttgatcttgtgtctgttttgaaaattgaaatgcagGACGCTGCCGCTTGGCTTGAATACTTTGAATCAAAAGTTATCGAGCAACAGGAAGCTGCACGCAATGGAACTCGGAAACCTGATGCATCAATTGCTAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC