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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_Os07g24190.1
intron # 10
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctacacaagttatttaattttcttgcagtttatctaacatttgcttgttacagATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACTGGATGTGTCTTTAGAAGGCAGGCATTGTATGGTTATGATGCCCCCAAAA
                                 atctaac  putative branch site (score: 2)
                                         tttgctt  CT-rich tract
        aagttatttaattttc  TA-rich tract