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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatactcatgacacttctggcgttgcttgtacatattgaccagttctttaaggctgtaatcctttaataatgctatgtccattttcagGCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAG

Basic information

species Oryza sativa
transcript LOC_Os07g37740.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G448715_T02 (Zea mays), 3'ss of exon 7
gtatactcatgacacttctggcgttgcttgtacatattgaccagttctttaaggctgtaatcctttaataatgctatgtccattttcagGCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAG
||||||| ||     || ||  |||  ||||   |  |    | || |   |||||   ||  || || | ||   |  |||||| |||| || ||||| |||||  ||||||| || |||||||| ||||| |||||||||||||||||||| |||||||| |||||||||||||| |||||
gtatactgat--tcattttgatgttatttgtg-gttctataaaattgtcccaggctcacatt-ttcaaaattgtattaaccattt-cagGTGTTAAGATCTGGTTATTGGCAATAATTTACTTCATATCTGGTGTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTGTATAATGCAATGAG

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 7
gtatactcatgacacttctggcgttgcttgtacatattgaccagttctttaaggctgtaatcctttaataatgctatgtccattttcagGCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAG
||||||| |  |   || ||| |||  ||||   | |  | || || | |   |||   |  |||||| | ||      || ||||||||||| ||||| |||||| ||||||| ||||||||||| ||||| |||||||||||||||||||| |||||||| ||||| |||||||| |||||
gtatactga--atcattttggtgttatttgttgttct--atcaattatatcgtgctc--acactttaa-attgtatcaaccgttttcagGCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG
















Mapped 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|58598584|gb|CK009112.1|CK009112
EST:     TCTCTTCTGGAACGTCATAGCAGTTACTTCAGCTTGGGTCAAGGGGGAAG                         GCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCT
genomic: TCTCTTCTGGAACGTCATAGCAGTTACTTCAGCTTGGGTCAAGGGGGAAGgtatactcat ... ccattttcagGCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCT
EST: gi|66923956|gb|CX110804.1|CX110804
EST:     TCTCTTCTGGAACGTCATAGCAGTTACTTCAGCTTGGGTCAAGGGGGAAG                         GCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTG
genomic: TCTCTTCTGGAACGTCATAGCAGTTACTTCAGCTTGGGTCAAGGGGGAAGgtatactcat ... ccattttcagGCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTG

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: 63 (upstream exon), 53 (downstream exon)
Score: 13

GATTGGCTTGCTGTCTCTTCTGGAACGTCATAGCAGTTACTTCAGCTTGGGTCAAGGGGGAAGgtatactcat ... ccattttcagGCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgaccagttctttaaggctgtaatcctttaataatgctatgtccattttcagGCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAG
                                            tccattttc  CT-rich tract
                       taatcctttaataat  TA-rich tract