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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttgccccatatttctgagatactctcctacacaagttatttaattttcttgcagtttatctaacatttgcttgttacagATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACTGGATGTGTCTTTAGAAGGCAGGCATTGTATGGTTATGATGCCCCCAAAA

Basic information

species Oryza sativa
transcript LOC_Os07g24190.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G025231_T01 (Zea mays), 3'ss of exon 10
gtaagatttgcc--ccatatttctgagatactctcctacacaagttatttaattttc--ttgcagtttatctaacatttgcttgttacagATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACTGGATGTGTCTTTAGAAGGCAGGCATTGTATGGTTATGATGCCCCCAAAA
|||||||||  |   |||||||||||| |  |||  |    |   ||| || |  |   |    ||||  ||||||||||  |  | ||||||||||||||||| ||||||||||| || || || || |||||||||||||||||||| ||||||||||||||||| ||||||||||||||||||||||
gtaagatttagcattcatatttctgaggtgttctgttgtctataatatgtattccttggtgaatgttttactaacatttgtgttgtgcagATCAACATGAAAGGTTTGGATGGTATTCAGGGTCCAATTTATGTTGGTACTGGATGTGTATTTAGAAGGCAGGCATTATATGGTTATGATGCCCCCAAAA

upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G028353_T02 (Zea mays), 3'ss of exon 10
gtaagatttgcc--ccatatttctgagatactctcctacacaagttatttaattttcttgcag----tttatctaacatttgcttgttacagATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACTGGATGTGTCTTTAGAAGGCAGGCATTGTATGGTTATGATGCCCCCAAAA
|||||||||| |   ||||||||||||||  |||  |    |  |||| || ||||||||  |    |||  ||||||||||     | ||||||||||||||||| ||||||||||| || || || || |||||||||||||||||||| ||||||||||||||||| ||||||||||||||||||||||
gtaagatttgacattcatatttctgagatgttctgttgtctacattatgtatttttcttggtgaatgttttactaacatttgtgctgtgcagATCAACATGAAAGGTTTGGATGGTATTCAGGGTCCGATTTATGTTGGTACTGGATGTGTGTTTAGAAGGCAGGCATTATATGGTTATGATGCCCCCAAAA

upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G47420.1 (Glycine max), 3'ss of exon 12
gtaagatttgccccatatttctgaga--tactctcctacacaagttatttaattttcttgcagtttatctaacatttgcttgttacagATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACTGGATGTGTCTTTAGAAGGCAGGCATTGTATGGTTATGATGCCCCCAAAA
||| || |   |  | |      | |  || |    |  |       | ||| |    |  |  | | ||||   |    | ||  |||| ||||||||||||||||||||||| ||||| || |  ||| |||| || |||||||| ||||| ||||| ||| | ||||||| |||| | || | ||
gtatgaatactctaagaaaaacaaaaattatttatttgaatttccattctaaatggaattgaaataaactaattctcttctcttttagATTAACATGAAAGGCTTGGATGGTATACAAGGACCTACATATATTGGGACAGGATGTGTTTTTAGGAGGCAAGCACTCTATGGTTTTGATTCTCCAAGAA

upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv18s0122g00120.t01 (Vitis vinifera), 3'ss of exon 10
---------------gtaagatttgccccatat-ttctgagatactctcctaca--caagttat-ttaattttcttgca-------gtttatctaacatttgcttgttacagATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACTGGATGTGTCTTTAGAAGGCAGGCATTGTATGGTTATGATGCCCCCAAAA
                |     ||||| ||| | |||||   | || | ||     |   | |  | |||| ||||| |         | || |   |  |     || ||||| ||||||||||| || ||||| || ||||| ||||| |||||||| ||||||||||| || |||||||| ||  | |||||||||||||| || || |
gtgagcatgcacttctttcatattgcctcatttcttctgctgttcttttctttgttctcataacatcaattatcttgtatgccaagactaatttgcaaactctactttccagATTAACATGAAAGGTTTAGATGGCATTCAAGGACCCATATATGTTGGGACTGGATGTGTGTTCAGAAGGCAAGCGCTATATGGTTATGATGCTCCAAAGA

upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 10
gtaagatt----tgccccatatttctgagatactctcctacacaagttatttaattttcttgcagtttatctaaca--tttgcttgttacagATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACTGGATGTGTCTTTAGAAGGCAGGCATTGTATGGTTATGATGCCCCCAAAA
|||||  |    | | |||||| |    ||| ||    |  | |  |||     ||||||  |  || |  |      |||   ||    |||||||||||||||||||||| || || ||||| ||||| ||||| |||||||| |||||||||||||| |||||||| |||||| ||||||| || ||||
gtaagcctgcagttctccatatctt---gatgctagttttgatagtttaga-gcttttctatcgattgacttggtcattttatatgcactagATCAACATGAAAGGCTTGGACGGAATTCAAGGACCCATTTATGTGGGTACTGGGTGTGTCTTTAGAAGACAGGCATTCTATGGTAATGATGCTCCAAAAA

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|29632757|gb|CB637766.1|CB637766
EST:     ACGTGGTCTTCTTCCAT                         ATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACT
genomic: ACGTGGTCTTCTTCGATgtaagatttg ... cttgttacagATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACT
EST: gi|29674793|gb|CB671068.1|CB671068
EST:     GGATTGATCGTCATGATCGATACGCCAACAGGAACGTGGTCTTCTTCGAT                         ATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACT
genomic: GGATTGATCGTCATGATCGATACGCCAACAGGAACGTGGTCTTCTTCGATgtaagatttg ... cttgttacagATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACT

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: 64 (upstream exon), 72 (downstream exon)
Score: 61

TTTGGTTGGAAAGAAGGTTTGTTATGTGCAATTCCCTCAAAGGTTTGATGGGATTGATCGTCATGATCGATACGCCAACAGGAACGTGGTCTTCTTCGATgtaagatttg ... cttgttacagATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACTGGATGTGTCTTTAGAAGGCAGGCATTGTATGGTTATGATGCCCCCAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctacacaagttatttaattttcttgcagtttatctaacatttgcttgttacagATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACTGGATGTGTCTTTAGAAGGCAGGCATTGTATGGTTATGATGCCCCCAAAA
                                 atctaac  putative branch site (score: 61)
                                         tttgctt  CT-rich tract
        aagttatttaattttc  TA-rich tract