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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGTGGGGAAGAAAGTGTGCTATGTGCAGTTCCCTCAGAGGTTTGATGGTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGATgtaagattcagcctctctggtactaagaccttgtggtctatattatgcttgttactattatggttcctaatatttgcattgtacag

Basic information

species Oryza sativa
transcript LOC_Os07g14850.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14850.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G082580_T01 (Zea mays), 5'ss of exon 8
TTTGGTGGGGAAGAAAGTGTGCTATGTGCAGTTCCCTCAGAGGTTTGATGGTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGATgtaagattcagcctctctggt---actaagaccttgtggtct--atattatgcttgttactat-tatggttcctaatatttgcattgtacag
||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| |||||||||||||||||| ||||||| |||||||| ||||||||||||||| || ||| |   || || |||||  | |||   | ||||  |   |   |  |||| || |||| | ||||||  |||||
TTTGGTGGGGAAGAAAGTGTGCTATGTACAGTTCCCTCAGAGGTTCGATGGTATTGACCGTCATGATCGATATGCTAACAGGAACGTCGTCTTTTTTGATgtaagattcagcttccctgttccaacaaacaccttaagctcttcgttttattgtccatgtcacatatgttttctaacacttgcatgatacag

upper sequence: LOC_Os07g14850.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G177631_T01 (Zea mays), 5'ss of exon 8
TTTGGTGGGGAAGAAAGTGTGCTATGTGCAGTTCCCTCAGAGGTTTGATGGTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGATgtaagattcagcctctctggt---actaagaccttgtggtctatattatgcttgttactattatggttcctaatatttgcattgtacag
||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||  | |||||||||| |||||| |||||||||||||||| || |||||||||| | || ||| |   ||  | |||||  | |||  ||| |  ||||   | |      |  |  |  |  ||   | |||
TTTGGTGGGGAAGAAAGTGTGCTATGTACAGTTCCCTCAGAGGTTTGATGGTATTGACAAAAATGATCGATACGCTAACAGGAACGTTGTCTTTTTTGACgtaagattcaacttccctgttcgaacacacaccttaagctcttcatttta-ttgtcgatgtctcatattttttttgtaacacc-tgcag

upper sequence: LOC_Os07g14850.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 5'ss of exon 10
TTTGGTGGGGAAGAAAGTGTGCTATGTGCAGTTCCCTCAGAGGTTTGATGGTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGATgtaagattcagcctctc-------tggtactaagaccttgtggtctatattatgcttgttactattatggttcctaatatttgcattgtacag
  || |||| ||||||||||||||||| |||||||| |||||||||||||| |||||  | |||||||||||||||||||||||| |||| || || ||||||||  |     ||||       || | ||| |   |  | || || |   |   | |   |    | | || |  ||| |||| |      
ACTGCTGGGAAAGAAAGTGTGCTATGTTCAGTTCCCACAGAGGTTTGATGGGATTGATAGGCATGATCGATATGCTAACCGGAACATTGTATTCTTTGATgtaagcctgcagttctccatatcttgatgcta-gttttgatagtttagagcttttctatcgattgacttggtcattttatatgcactag----

upper sequence: LOC_Os07g14850.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv18s0122g00120.t01 (Vitis vinifera), 5'ss of exon 10
TTTGGTGGGGAAGAAAGTGTGCTATGTGCAGTTCCCTCAGAGGTTTGATGGTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGATgtaagattcagcctctctggtactaagaccttgtggtctatattatgcttgttactattatggttcctaatat-ttgcattgtacag-------------------------
 ||| | || |||| ||| |||||||| |||||||| |||||||||||||||||||||  | ||||||||||||| ||||| |||  ||| || || ||||| ||  |   | ||| |  || |    | ||        | || |  |  ||  | | ||     | | ||| ||| ||   |                            
ATTGCTTGGAAAGAGAGTCTGCTATGTTCAGTTCCCCCAGAGGTTTGATGGTATTGACAAAAATGATCGATATGCCAACCGAAACACTGTTTTCTTTGATgtgagcatgcacttctttcatattgcctcatttcttctgctgttcttttctttgttctcataacatcaattatcttgtatgccaagactaatttgcaaactctactttccag

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|427599|gb|D23732.1|D23732
EST:     GTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGAT                         ATCAACATGAAAGGTCTGGATGGAATTCAAGGCCCCATCTATGTTGGTACT
genomic: GTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGATgtaagattca ... cattgtacagATCAACATGAAAGGTCTGGATGGAATTCAAGGCCCCATCTATGTTGGTACT
EST: gi|58672442|gb|CK061128.1|CK061128
EST:     GTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGAT                         ATCAACATGAAAGGTCTGGATGGAATTCAAGGCCCCATCTATGTTGGTACT
genomic: GTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGATgtaagattca ... cattgtacagATCAACATGAAAGGTCTGGATGGAATTCAAGGCCCCATCTATGTTGGTACT
EST: gi|58663832|gb|CK052518.1|CK052518
EST:     GTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGAT                         ATCAACATGAAAGGTCTGGATGGAATTCAAGGCCCCATCTATGTTGGTACT
genomic: GTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGATgtaagattca ... cattgtacagATCAACATGAAAGGTCTGGATGGAATTCAAGGCCCCATCTATGTTGGTACT
EST: gi|427628|gb|D23761.1|D23761
EST:     GTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGAT                         ATCAACATGAAAGGTCTGGATGGAATTCAAGGCCCCATCTATGTTGGTACT
genomic: GTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGATgtaagattca ... cattgtacagATCAACATGAAAGGTCTGGATGGAATTCAAGGCCCCATCTATGTTGGTACT
EST: gi|58667198|gb|CK055884.1|CK055884
EST:     GTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGAT                         ATCAACATGAAAGGTCTGGATGGAATTCAAGGCCCCATCTATGTTGGTACT
genomic: GTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGATgtaagattca ... cattgtacagATCAACATGAAAGGTCTGGATGGAATTCAAGGCCCCATCTATGTTGGTACT

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: 75 (upstream exon), 73 (downstream exon)
Score: 26

TTTGGTGGGGAAGAAAGTGTGCTATGTGCAGTTCCCTCAGAGGTTTGATGGTATTGACCGACATGATCGATATGCTAACCGGAACGTTGTCTTTTTCGATgtaagattca ... cattgtacagATCAACATGAAAGGTCTGGATGGAATTCAAGGCCCCATCTATGTTGGTACTGGATGTGTCTTCAGACGGCAAGCTCTCTATGGTTATGATGCGCCAAAAA




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