Sequence
atgc intronic sequence ATGC exonic sequence...taattttatcactggacaagttcaaaaatccacaaacttgacacagttaattagtggaacacaaaacatgatgatgttaagtgatgtgtttattttgtagCTGGATGGAACAATTGTAGCCCCAACCAGTGCTAAAGCTTGGGATTCTGGTTTGCTTCAATGGATTGAGTTTACAAAACTAAATGGAGTATCAATTCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g45060.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g45060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G179696_T03 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------taattttatca--------ctggacaagttcaaaaatccacaaacttgacacagttaattagtggaacacaaaac-------atgatgatgttaagtgatgtgtttattttgtagCTGGATGGAACAATTGTAGCCCCAACCAGTGCTAAAGCTTGGGATTCTGGTTTGCTTCAATGGATTGAGTTTACAAAACTAAATGGAGTATCAATTCAAG
| | || | || | ||| | | | | | || |||| | | | | ||||| | || | ||| |||| | || ||| | | |||| ||||||| |||||||| |||| ||||||||||||||| | |||| ||| || ||||| || ||| | ||||| || |||||||||||| | |||||||
gtaagcatgttctttatcccaaatgataagatacttaaaagggttttctcaacatagcttgaattgagcaacaaaaggcaggatgggattgtattttatctaatttgagat-gcacaccaatggaagaataagttcgttgagtaatgctgtttaatgttgtactcactttgcagCTGGAAGGAACAATCCTAGCTCCAACCAGTGCTAAATCCTGGGGTTCAGGCTTGCTCCAGTGGCTCGAGTTCACCAAACTAAATGGAATGGTTATTCAAG
upper sequence: LOC_Os01g45060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G037431_T01 (Zea mays), 3'ss of exon 2
-taattttatcactggac--aagttcaaaaatccacaaa--------cttgacacagtt--aattagtggaacacaaaacatgatgatgtta-agtgatgtgtttattttgtagCTGGATGGAACAATTGTAGCCCCAACCAGTGCTAAAGCTTGGGATTCTGGTTTGCTTCAATGGATTGAGTTTACAAAACTAAATGGAGTATCAATTCAAG
|||| || | | || | | || || |||||| | || || | |||| | | | | ||| || | || ||| | |||||| || |||| |||||||| |||| |||| |||||||||| | |||| |||||| ||||| || ||| | ||||| || ||||||||||| || |||||||
gtaatcctactcgtaatcccaaatgctaagatacacaaaagggccttttcaacgtagcttgaattgaccaacaaagtaggacaatggagtagtaatgttgtactcattttgcagTTGGAAGGAACAATCCTAGCTCCAATCAGTGCTAAATCCTGGGGTTCTGGCTTGCTCCAGTGGCTCGAGTTCACCAAACTAAATGGGATAGTTATTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttaattagtggaacacaaaacatgatgatgttaagtgatgtgtttattttgtagCTGGATGGAACAATTGTAGCCCCAACCAGTGCTAAAGCTTGGGATTCTGGTTTGCTTCAATGGATTGAGTTTACAAAACTAAATGGAGTATCAATTCAAG
agttaat putative branch site (score: 4)
tttatttt putative PPT
tttattttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taattttatcactggacaagttcaaaaatccacaaacttgacacagttaattagtggaacacaaaacatgatgatgttaagtgatgtgtttattttgtagCTGGATGGAACAATTGTAGCCCCAACCAGTGCTAAAGCTTGGGATTCTGGTTTGCTTCAATGGATTGAGTTTACAAAACTAAATGGAGTATCAATTCAAG
- - - - - -ctggaca
- - - - - - - - - - - caaaaat
- - - - - - - - - - - - - - -ccacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgatg