Sequence
atgc intronic sequence ATGC exonic sequenceGTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATGgtaatcttttctcatctttcattatctattcttctctatggtgttttgtctctaccaaattttatagggcaattgtgtcatagctcaagactgattacgaatgactgatatctgtttgctaatgttctgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os12g40830.3 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G398107_T01 (Zea mays), 5'ss of exon 4
GTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATGgtaatcttttctcatctttcattatctattcttctctatggtgttttgtctctaccaaattttataggg-caat---tgtgtcatagctcaagactgattacgaatgactgatatctgtttgctaat-------gttctgcag
|||| || || | ||||||||||||| |||| | |||||||||||||||||||||||||||||||||||||| |||||||| ||||| |||||| |||||| |||| ||| | | || ||| || |||||| || ||| ||| || ||||| || ||| || || | ||| | || ||||||||||| || |||||
GTTACATAGGCCCGGTTTCCTTTTTAAATACTATGCTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGACCTTGTATACGgtaaccttttcccatcttctgttatttatgtgctt-------gcttcttctttagtaaatttaattgggacaagatacgtctcataactagagattggctaggcatggttcattcttgtttgctaattgcaaacattatgcag
upper sequence: LOC_Os12g40830.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G069758_T02 (Zea mays), 5'ss of exon 6
GTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATGgtaatcttttctcatctttcattatctattcttctctatggtgttttgtctctaccaaattttataggg-caatt-gtgtcatagctcaagactgattacgaatgactgata--tctgtttgctaat-------gttctgcag
||||||| || || |||||||||||| |||||| |||||||||||||| ||||| |||||||| |||||||||||||||||||||||||||||||||||||| |||| | | | | | ||| | | ||||| | |||| ||||| ||||||||| ||||||| || ||| | || ||||||||||||| | ||||||
GTTATATAGGCTCAGTTTCCTTTTTAGATACTGTGCTACAAGTTGTTGAGAAATTGCGATCAGTTAATCCTGATCTTGTATATGgtaatcttttctcatcttttgttatttgtatgcttgcttcttctttaataa--atttaatttaacagggacaatttaggtcatagctagagactgactagacatggttaattcttctgtttgctaattgcaaacatgctgcagMapped 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|568331|gb|D39176.1|D39176EST: CTGATCTTGTATATG TTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATT
genomic: CTGATCTTGTATATGgtaatctttt ... tgttctgcagTTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATT
EST:
gi|58661072|gb|CK049752.1|CK049752EST: ACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATG TTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATT
genomic: ACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATGgtaatctttt ... tgttctgcagTTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATT
EST:
gi|66924011|gb|CX110859.1|CX110859EST: ACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATG TTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATT
genomic: ACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATGgtaatctttt ... tgttctgcagTTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATT
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:
72 (upstream exon),
60 (downstream exon)
Score:
28GTTATATTGGATCTGTTTCCTTTTTAACTACTGTACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATGgtaatctttt ... tgttctgcagTTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATTTAATATCTGTTTATCAACAGAAG
<
<
<