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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcaatttgtttcatctcctgccttccagttttccattcttaatatggcatgattttatctttgctggaacagaatgttgtttaataccatttgttccaaaacatatcattcactgacactaccattatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAGCATATCTACAACCTATATGTGGAATATGTTGTAAAAAATCCTTTGTACG

Basic information

species Oryza sativa
transcript LOC_Os01g33020.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g33020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G010146_T01 (Zea mays), 3'ss of exon 2
gttagtcaatttgtttcatctcctgccttccagttttccattcttaatatggcatgattttatctttgctggaacagaatgttgtttaataccatttgttccaaaac-atatcat-tcactgacactaccattatg-tgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAGCATATCTACAACCTATATGTGGAATATGTTGTAAAAAATCCTTTGTACG
                                  |   ||||  |  | | ||||| |        || | |  ||||  | |||  ||||    ||  |||| | | |||   | | ||  ||  |||| |  || |||||||||| ||||||||||||||||||||||||||||| || ||| |||| ||||||||||||||||||||||||||||| ||||||||||||||| |||| |
----------------------------------tggtcatttct--tttagcatggtag------tgatcgtgcagatagatgtacaatattcctttctccagagctatactctatgacctactataccctgttggtgtagCTTATACTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATCTACAACCTATATGTGGAATACGTTGTAAAAAATCCTCTGTATG

upper sequence: LOC_Os01g33020.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G039373_T01 (Zea mays), 3'ss of exon 2
gttagtcaatttgtttcatctcctgccttccagttttccattcttaatatggcatgattttatctttgctggaacagaatgttgtttaat-accatttgttccaaaacatatcattcactgacactaccattatg-tgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAGCATATCTACAACCTATATGTGGAATATGTTGTAAAAAATCCTTTGTACG
                                 ||   ||||  || | | ||||| |         | | || ||||  | |||  | | |   |||  |||| | |    |  | ||| || ||||| |  || ||||||||||  |||||||||||||||||||||||||||| || ||| |||| |||||||| ||||| |||||||||||||||||||||||||||||| |||| |
---------------------------------ttggtcatt--tattttagcatggtag------cgatcgagcagatagatgtacagttattttttcctccagagctatactctgacttactctaccctcttggtgtagCTTATATTAATTACACATCCAAGGACTGGTGATCAGCGAGACTCGCTAAAGCATATATACAATCTATATGTGGAATATGTTGTAAAAAATCCTCTGTATG
















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|88832255|gb|CI017489.1|CI017489
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|88956108|gb|CI092396.1|CI092396
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|88968596|gb|CI098826.1|CI098826
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|88988903|gb|CI040635.1|CI040635
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|58589387|gb|CF987695.1|CF987695
EST:     AGACAAACACATACAAATGGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|86520090|gb|CI160296.1|CI160296
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|87028415|gb|CI263757.1|CI263757
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|89168502|gb|CI038856.1|CI038856
EST:     AGACGAACACATACCAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|88239868|gb|CI239030.1|CI239030
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|86869390|gb|CI339114.1|CI339114
EST:     TAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: TAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|86544227|gb|CI184433.1|CI184433
EST:     TGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CGTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: TGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|87034968|gb|CI188771.1|CI188771
EST:     AGACAGACACATACGAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATGACACATGCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|88832263|gb|CI017497.1|CI017497
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|58658081|gb|CK046761.1|CK046761
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|163928213|gb|EG712541.1|EG712541
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|9865647|gb|AU101397.1|AU101397
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|218485437|gb|FG946454.1|FG946454
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|89199179|gb|CI255445.1|CI255445
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|218488359|gb|FG945110.1|FG945110
EST:     AGACAAACACATACAAATTGAACTTTCTAGAGAGCCCTGCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|88982282|gb|CI027859.1|CI027859
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
EST: gi|58599380|gb|CK009908.1|CK009908
EST:     AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAG                         CTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG
genomic: AGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAG

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: 61 (upstream exon), 17 (downstream exon)
Score: 3

TCTTGGGGTGCCACTACTGCCGGGCCAGGGTTGCTCATTTTACAGCTTCAAGACAAACACATACAAATTGAACTTCCTAGAGAGCCCTTCTGGTATCAAGgttagtcaat ... ttatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAGCATATCTACAACCTATATGTGGAATATGTTGTAAAAAATCCTTTGTACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaataccatttgttccaaaacatatcattcactgacactaccattatgtgtagCTTATTCTAATTACACATCCAAGGACTGGTGATCAACGTGACACGCTGAAGCATATCTACAACCTATATGTGGAATATGTTGTAAAAAATCCTTTGTACG
                               cactgac  putative branch site (score: 3)
                  aaaacatat  TA-rich tract