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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcgtgatttttttttcttgaaccaataacattcttgtttctatgatattatctttacctggaatcttttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACTGCTGACCAATATAGATACCCTGATGTCCCATCCTTTCTGGTGTATATAC

Basic information

species Oryza sativa
transcript LOC_Os07g06950.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G018508_T03 (Zea mays), 3'ss of exon 17
gtatggcgtgattttt---ttttcttgaaccaataacattcttgtttctatgatattatctttacctgga---atcttttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACTGCTGACCAATATAGATACCCTGATGTCCCATCCTTTCTGGTGTATATAC
|||     ||||| |    || | |        ||     ||||||| | ||||| | || |||| ||||   || |||||    |||||||||||||| |||||  | ||||||||||||||| ||||| |||||| |||||||| |||| |||  ||||| || ||||||||| ||  ||||||||
gtaaatgctgattgtaaggttgtttctgcttggtattgaacttgtttttgtgatact-tccttacatggactcattttttgttagcagCTTGAAGATGGGGACATAATCTGTTTTCAAAAATCTTCAAAGGCAGATAGTGCTGACCGATATCGATTTCCTGACGTACCATCCTTTTTGACGTATATAC

upper sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM5G864266_T01 (Zea mays), 3'ss of exon 23
gta-tggcgtgatttttttttcttgaaccaataacattcttgtttctatgatattatctttacctggaatcttttgcgt--acagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACTGCTGACCAATATAGATACCCTGATGTCCCATCCTTTCTGGTGTATATAC
||| ||  | |  |    ||  ||| ||  | | ||| |||||   | ||||  | |  | || ||||  | ||   ||   ||||||||||| || || ||  |||||||||||||  || |||| ||||||| ||| |||| |||| |||  ||||| |||||||||||| ||  ||||||||
gtaatgctgagtgtcaggttgtttgtacttaaatcatacttgt---tgtgatgct-ttctaacgtggacccattcatgttcgcagCTTGAAGACGGGGATATAATTTGTTTTCAAAAGCCTTCAAAACCAGATAGTGCAGACCGATATCGATTTCCTGACGTCCCATCCTTTTTGACGTATATAC
















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|58661271|gb|CK049951.1|CK049951
EST:     ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAG                         CTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
genomic: ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAGgtatggcgtg ... ttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
EST: gi|66922652|gb|CX109500.1|CX109500
EST:     ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAG                         CTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
genomic: ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAGgtatggcgtg ... ttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
EST: gi|58659867|gb|CK048547.1|CK048547
EST:     ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTGGCCAG                         CTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
genomic: ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAGgtatggcgtg ... ttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
EST: gi|27577375|gb|CB000070.1|CB000070
EST:     ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAG                         CTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
genomic: ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAGgtatggcgtg ... ttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
EST: gi|58667338|gb|CK056024.1|CK056024
EST:     ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAG                         CTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
genomic: ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAGgtatggcgtg ... ttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
EST: gi|58656552|gb|CK045232.1|CK045232
EST:     ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAG                         CTGGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
genomic: ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAGgtatggcgtg ... ttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
EST: gi|58674203|gb|CK062889.1|CK062889
EST:     ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAG                         CTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
genomic: ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAGgtatggcgtg ... ttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
EST: gi|58654004|gb|CK042684.1|CK042684
EST:     ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGGCAG                         CTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
genomic: ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAGgtatggcgtg ... ttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
EST: gi|58658981|gb|CK047661.1|CK047661
EST:     ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCGTGCCAG                         CTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
genomic: ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAGgtatggcgtg ... ttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
EST: gi|163920232|gb|EG710577.1|EG710577
EST:     ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAG                         CTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT
genomic: ATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAGgtatggcgtg ... ttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACT

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: 67 (upstream exon), 73 (downstream exon)
Score: 27

GAAATCAAGTTTGAGCCCAATGTAATGTGTGAATATATTGACAATAGGCTTCTATTTCGAGCTTGCCAGgtatggcgtg ... ttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACTGCTGACCAATATAGATACCCTGATGTCCCATCCTTTCTGGTGTATATAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caataacattcttgtttctatgatattatctttacctggaatcttttgcgtacagCTTGAAGATGGTGACATCGTTTGTTTTCAAAAATCTCCAAAGCCAGATACTGCTGACCAATATAGATACCCTGATGTCCCATCCTTTCTGGTGTATATAC
 caataac  putative branch site (score: 27)
                                         tcttttgc  putative PPT
                  tatgatattatcttta  TA-rich tract