Sequence
atgc intronic sequence ATGC exonic sequencegtatggtgtaatcttatcttttatttttactcgcctgtctacttttaagaaacttttcctctcttactgatacgtcattgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCAGAGCGGTTAAAACTGTCCACTGTACACGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g60040.1 |
intron # | 29 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 29
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 28
gtatggtgtaatcttatcttttatttttactcgcctgtctactt--ttaagaaacttttcctctcttactga-tacgtcattgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCAGAGCGGTTAAAACTGTCCACTGTACACGAAG
||||| | | | || || || | || | || | || | | ||| || || ||||| | | || |||||||| | ||||||||||||||||||||||||||||||||| |||||| |||| || | |||||||| |||||||| ||||
gtatgtttca--tctgcctattccattcattcatatttccatttaatgctgcaacattctaactacaactgaatttattgtttggtgtagGTTGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCTATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG
upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 29
lower sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 11
gtatggtgtaatcttatcttttatttttactcgcctgtctactt--ttaagaaacttttcctctcttactga-tacgtcattgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCAGAGCGGTTAAAACTGTCCACTGTACACGAAG
||||| | | | || ||| ||| | || || || | || | | | | || | | ||||| | | || |||||| | | |||||||||||||||||||||||||||||||||||||||| |||| || | |||||||| |||||||| ||||
gtatgtttca--tccacctattactttcattcatctttccatttaatgctgcagcattctcccaacaactgaatttattgtttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAGMapped 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|88370934|gb|CI595046.1|CI595046EST: CTGCTGAATCCTTTATGAATGAAATTCTCAAGATTTGTGGCCAAGATGTG GTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAAGATTTGTGGCCAAGATGTGgtatggtgta ... ttgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCA
EST:
gi|58686785|gb|CK075472.1|CK075472EST: CTGCTGAATCCTTTATGAATGAAATTCTCAAGATTTGTGGCCAAGATGTG GTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAAGATTTGTGGCCAAGATGTGgtatggtgta ... ttgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
74 (upstream exon),
69 (downstream exon)
Score:
46GATAAATCTTCTGAAGTTCGTAAAGCTGCTGAATCCTTTATGAATGAAATTCTCAAGATTTGTGGCCAAGATGTGgtatggtgta ... ttgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCAGAGCGGTTAAAACTGTCCACTGTACACGAAG
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcctgtctacttttaagaaacttttcctctcttactgatacgtcattgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCAGAGCGGTTAAAACTGTCCACTGTACACGAAG
ttttaagaaactttt TA-rich tract