Sequence
atgc intronic sequence ATGC exonic sequenceAATTCAGTGAAGTCTTTGTTCACCAGCTGATCCACACAATTGAGTTTGTGCTCGGTGCAGTCTCAAATACAGCCTCTTACCTTCGTCTTTGGGCTCTTAGgtacctctgaacttacatgatacataacaatgccacctcttaatgtcacatggaagaaattgacggttgagtaattctattgttcgtgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os10g10500.1 |
intron # | 16 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g10500.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA11G12120.1 (Glycine max), 5'ss of exon 16
AATTCAGTGAAGTCTTTGTTCACCAGCTGATCCACACAATTGAGTTTGTGCTCGGTGCAGTCTCAAATACAGCCTCTTACCTTCGTCTTTGGGCTCTTAGgtacctctgaa---cttacatgatacataacaatgccacctcttaa-tgtcacatggaagaaatt--gacggttgagtaat----tctattgttcgtgcag---------------------------------------------------------------------------------
| ||||| ||||||||||| || || || || || || || || ||||| || || |||||||| |||||||| |||||||| ||||| ||||| |||||||| ||| | | | | | | || ||| | ||| | | ||| | || || | || | | || | |||| | || |
AGTTCAGCGAAGTCTTTGTACATCAACTCATACATACCATAGAATTTGTACTTGGAGCAGTCTCTAATACAGCTTCTTACCTCCGTCTATGGGCCCTTAGgtatgtctataagtcccaaacgttctattctaatagtaatgcttgagtcccactagaaacaaggttggaacctcacatcatgcagtttattacttttgtatatctattcgtctatagatatgtttgatgcatgtattgaattgctttgcacatttactgatgttttccttttctgtacccag
upper sequence: LOC_Os10g10500.1 (Oryza sativa), 5'ss of exon 16
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 5'ss of exon 16
AATTCAGTGAAGTCTTTGTTCACCAGCTGATCCACACAATTGAGTTTGTGCTCGGTGCAGTCTCAAATACAGCCTCTTACCTTCGTCTTTGGGCTCTTAGgtac------------------------ctctga-----acttacatgata--cataacaatgc---cacctcttaatgtcacatggaagaaattgacggttgagtaattctattgttcgtgcag-------------------------------------------------------------------
||||||| ||| ||||||| ||||| || || ||||| |||||||||||||| || || || || || || || ||||| |||||||| |||||||| |||||| |||| | ||| |||| | || ||| | ||| | | ||| ||| | | || | | | ||| | | | || || ||
AATTCAGCGAAATCTTTGTGCACCAACTCATTCACACCATTGAGTTTGTGCTTGGAGCTGTTTCCAACACTGCTTCTTATCTTCGTCTCTGGGCTCTCAGgtacaaaatactacttgctttcaaatagtcctgattgtcatctaccagatagtcctaccaaaactagcacttgtcaatatcatctagcagtagtattctgttaaattcattggttcttgatggcttaatgtcgaagtattggtttgcgcatttcgtgactaatctttatgctttgctgggattcctattcag
upper sequence: LOC_Os10g10500.1 (Oryza sativa), 5'ss of exon 16
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 16
AATTCAGTGAAGTCTTTGTTCACCAGCTGATCCACACAATTGAGTTTGTGCTCGGTGCAGTCTCAAATACAGCCTCTTACCTTCGTCTTTGGGCTCTTAGgtacctctgaacttacatgatacataacaatgccacctcttaatgtcacatggaagaaattgacggttgagtaattctattgttcgtgcag
||||||| || | ||||| || |||||||| ||||| || ||||||||||| || || || || || || || |||||||| ||||| |||||||| ||||| | || | | || | | ||| |||| | | | || | | || | | || | |||
AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatgagtag---tagaagctatacatgaat---------------tacataacctatactcgtggcttaatatccattcttttgtttcagMapped 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|58690466|gb|CK079153.1|CK079153EST: CTCGGTGCAGTCTCAAATACAGCCTCTTACCTTCGTCTTTGGGCTCTTAG TCTTGCACACTCGGAGCTGTCCACTGTCTTCTACGAGAAAGTTCTTGTTCT
genomic: CTCGGTGCAGTCTCAAATACAGCCTCTTACCTTCGTCTTTGGGCTCTTAGgtacctctga ... gttcgtgcagTCTTGCACACTCGGAGCTGTCCACTGTCTTCTACGAGAAAGTTCTTGTTCT
EST:
gi|218497346|gb|FG955378.1|FG955378EST: CTCGGTGCAGTCTCAAATACAGCCTCTTACCTTCGTCTTTGGGCTCTTAG TCTTGCACACTCGGAGCTGTCCACTGTCTTCTACGAGAAAGTTCTTGTTCT
genomic: CTCGGTGCAGTCTCAAATACAGCCTCTTACCTTCGTCTTTGGGCTCTTAGgtacctctga ... gttcgtgcagTCTTGCACACTCGGAGCTGTCCACTGTCTTCTACGAGAAAGTTCTTGTTCT
EST:
gi|58592918|gb|CF991226.1|CF991226EST: CTCGGTGCAGTCTCAAATACAGCCTCTTACCTTCGTCTTTGGGCTCTTAG TCTTGCACACTCGGAGCTGTCCACTGTCTTCTACGAGAAAGTTCTTGTTCT
genomic: CTCGGTGCAGTCTCAAATACAGCCTCTTACCTTCGTCTTTGGGCTCTTAGgtacctctga ... gttcgtgcagTCTTGCACACTCGGAGCTGTCCACTGTCTTCTACGAGAAAGTTCTTGTTCT
EST:
gi|58605919|gb|CK033952.1|CK033952EST: CGGTGCAGTCTCAAGAGTACAGCCTCTTACCTTCGTCTTTGGGCTCTTAG TCTTGCACACTCGGAGCTGTCCACTGTCTTCTACGAGAAAGTTCTTGTTCT
genomic: CGGTGCAGTCTCAA-A-TACAGCCTCTTACCTTCGTCTTTGGGCTCTTAGgtacctctga ... gttcgtgcagTCTTGCACACTCGGAGCTGTCCACTGTCTTCTACGAGAAAGTTCTTGTTCT
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),
60 (downstream exon)
Score:
67AATTCAGTGAAGTCTTTGTTCACCAGCTGATCCACACAATTGAGTTTGTGCTCGGTGCAGTCTCAAATACAGCCTCTTACCTTCGTCTTTGGGCTCTTAGgtacctctga ... gttcgtgcagTCTTGCACACTCGGAGCTGTCCACTGTCTTCTACGAGAAAGTTCTTGTTCTATCATGGGG
<
<
<