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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaatctattttagtacttctactattatttacaacttccttatttttcttctactttactgatgcatccaaatgcagCTCAAAGGATTTGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATTGACCCTAGTAGAAAAG

Basic information

species Oryza sativa
transcript LOC_Os12g07190.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G126656_T01 (Zea mays), 3'ss of exon 6
gtgagcaatctattttagtacttctactattatttacaacttccttatttttcttc-tactttactgatgcatccaaatgcagCTCAAAGGATTTGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATTGACCCTAGTAGAAAAG
|| |||| ||||| ||||||   | | |||| |  |  |   | || |   | ||  |  | ||    |   | |   ||||||||||| ||| | ||||||||||||||  |||| ||| |||| ||||| ||||| ||||||||||||
gtaagcattctatgttagtaaaac-agtattgtccatgatccctttctaactgttggtgttgtataattatgttc---tgcagCTCAAAAGATATACTTATGCGTGTTGTGTCACAAAATATTTCCCCTGAGTTGACTCTAGTAGAAAAG

upper sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA05G32930.1 (Glycine max), 3'ss of exon 6
---gtgagcaatctattttagtacttctactattatttacaacttccttatttttcttctactttactg-----------atgcatccaa-----atgcagCTCAAAGGATTTGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATTGACCCTAGTAGAAAAG
    |   | |||      | | | |||  || |  |  || | | | || ||| |  ||   | | ||           |||  | | |     |||||| ||||||||  | || ||||||||||| || || |||||||||||||| ||||| || || ||||||
tgattttcccatccgccccaat-cctctgttactcatcccatccttcctaatttgcaccttaatcattgtaagatgcttaatgttttctatactcatgcagTTCAAAGGACATACTAATGCGTGTTGTGGCTCAAAATCTTTCTCCTGAGTTGACTCTCGTGGAAAAG

upper sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G00560.2 (Glycine max), 3'ss of exon 6
----------------------------------------------------------------------------------gtgagcaatctat----tttagtacttctactattatttacaactt----ccttatttttc-ttctactttact-gatgcatccaa-----atgcagCTCAAAGGATTTGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATTGACCCTAGTAGAAAAG
                                                                                  ||||  ||         ||| |    |  | |||||||  |   |     ||   ||  || || ||   | ||  |||| | | |     |||||| ||||||||  | || ||||||||||| || || |||||||||||||| ||||| || || ||||||
gtaagatctttttcagaggctttaatctcttcttttggaagttgagggtgtggaataatatacaaaattgcatgttttcgtagtgaagaactctcaaggtttggggtataaaatattattctctggtaggagccaggttaatcattgtaagatgcttaatgctttctatgctcatgcagTTCAAAGGACATACTAATGCGTGTTGTGGCTCAAAATCTTTCTCCTGAGTTGACTCTCGTGGAAAAG

upper sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv07s0031g02750.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------------------------gtgagcaatctatttta--gtacttctactattatttacaacttccttatttttcttctactttactgatgcatccaaat-gcagCTCAAAGGATTTGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATTGACCCTAGTAGAAAAG
                                                                         | ||||   | |      ||  ||  |    | |||| | || |      || ||| |   |   || | || | || | |||| ||||||||| | |||||||| ||||| ||||| || ||||||||||| ||||| || || ||||||
gtattattcatttctctactggctcctatcttttctgactgtaactttgtatcaacaaggttttatttttgcattagcagcatttcaggaggtgttttgatgtctgtttatatctactggtggttacttatgtctgtttgtttcaactaacttgcagTTCAAAGGATATTCTTATGCGGGTTGTGGCACAAAACCTTTCTCCTGAGTTGACTCTGGTGGAAAAG

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|29616351|gb|CB621363.1|CB621363
EST:     GTTAATTCGGTGGTTGTTGCTACAGGAAACACACTACAGGGGATCTTCAC                         CTCAAAGGATTTGCTTATGCGTNGT-GTTGCACAGAATCTTTCTCCTGAAT
genomic: GTTAATTCGGTGGTTGTTGCTACAGGAAACACACTACAGGGGATCTTCACgtgagcaatc ... ccaaatgcagCTCAAAGGATTTGCTTATGCGT-GTTGTTGCACAGAATCTTTCTCCTGAAT
EST: gi|29658205|gb|CB654480.1|CB654480
EST:     GTTAATTCGGTGGTTGTTGCTACAGGAAACACACTACAGGGGATCTTCAC                         CTCAAAGGATTTGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATT
genomic: GTTAATTCGGTGGTTGTTGCTACAGGAAACACACTACAGGGGATCTTCACgtgagcaatc ... ccaaatgcagCTCAAAGGATTTGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATT
EST: gi|58612797|gb|CK040509.1|CK040509
EST:     GTTAATTCGGTGGTTGTTGCTACAGGAAACACACTACAGGGGATCTTCAC                         CTCAAAGGATTCGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATT
genomic: GTTAATTCGGTGGTTGTTGCTACAGGAAACACACTACAGGGGATCTTCACgtgagcaatc ... ccaaatgcagCTCAAAGGATTTGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATT
EST: gi|29683887|gb|CB680162.1|CB680162
EST:     GTTAATTCGGTGGTTGTTGCTACAGGAAACACACTACAGGGGATCTTCAC                         CTCAAAGGATTTGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATT
genomic: GTTAATTCGGTGGTTGTTGCTACAGGAAACACACTACAGGGGATCTTCACgtgagcaatc ... ccaaatgcagCTCAAAGGATTTGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATT
EST: gi|58693946|gb|CK082633.1|CK082633
EST:     GTTAATTCGGTGGTTGTTGCTACAGGAAACACACTACAGGGGATCTTCAC                         CTCAAAGGATTTGCTTATGCG
genomic: GTTAATTCGGTGGTTGTTGCTACAGGAAACACACTACAGGGGATCTTCACgtgagcaatc ... ccaaatgcagCTCAAAGGATTTGCTTATGCG
EST: gi|29617498|gb|CB622510.1|CB622510
EST:     GTTAATTCGGTGGTTGTTGCTACAGGAAACACACTACAGGGGATCTTCAC                         CTCAAAGGATTTGCTTAT
genomic: GTTAATTCGGTGGTTGTTGCTACAGGAAACACACTACAGGGGATCTTCACgtgagcaatc ... ccaaatgcagCTCAAAGGATTTGCTTAT

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: 59 (upstream exon), 69 (downstream exon)
Score: 41

CTCCTTCAGACCCAGTGTATGTAGCAACACAGAAAATGCGTGAATTTCGAGTTAATTCGGTGGTTGTTGCTACAGGAAACACACTACAGGGGATCTTCACgtgagcaatc ... ccaaatgcagCTCAAAGGATTTGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATTGACCCTAGTAGAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatttacaacttccttatttttcttctactttactgatgcatccaaatgcagCTCAAAGGATTTGCTTATGCGTGTTGTTGCACAGAATCTTTCTCCTGAATTGACCCTAGTAGAAAAG
                                  tactgat  putative branch site (score: 41)
                 ttatttttcttcta  TA-rich tract