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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTAGATGAAGATGCAGTAGGATCAGTGGACCAACCTGGCTATGGAGCCAAGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatcttactaaatcctgtgaccttggcatactttatttttttgctacgtggtgtagcaagatcactttagatctataccatttgctgccaaaaccatagtaaatatgataattgtgacag

Basic information

species Zea mays
transcript GRMZM2G101791_T02
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101791_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os02g35630.1 (Oryza sativa), 5'ss of exon 14
TGTAGATGAAGATGCAGTAGGATCAGTGGACCAACCTGGCTATGGAGCCAAGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatcttactaaatcctgtgaccttggcatactttatttttttgctacgtggtgtagcaagatcactttagatctataccatttgctgccaaaaccatagtaaatatgataattgtgacag
|||||||||||| ||||| ||| ||||||||||||||||||  ||||| ||||| |||||||| || |||||||| || |  ||||| ||||| ||||||||||   || || ||| ||   | || |    | |  || |   |   |  ||       || ||  |||  |    ||||                                          
TGTAGATGAAGACGCAGTCGGAGCAGTGGACCAACCTGGCTGCGGAGCTAAGATCCTTTATGGCGATGGTGCTTTTGAACGTTATCTCTCCCAGATAAAGgtaaggatt-cttaattctacaaact-gatgga-tgcatatgcatataatctgcaactataatattccttggggaaaatactgcag-------------------------------------
















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|211488136|gb|FL062513.1|FL062513
EST:     AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAG                         GTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
genomic: AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
EST: gi|211488132|gb|FL062509.1|FL062509
EST:     AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAG                         GTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
genomic: AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
EST: gi|211127807|gb|FL448898.1|FL448898
EST:     AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAG                         GTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
genomic: AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
EST: gi|211488134|gb|FL062511.1|FL062511
EST:     AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAG                         GTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
genomic: AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
EST: gi|32867859|gb|CF007541.1|CF007541
EST:     AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAG                         GTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
genomic: AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
EST: gi|5608481|gb|AI902058.1|AI902058
EST:     AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAG                         GTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
genomic: AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
EST: gi|211221052|gb|FL468690.1|FL468690
EST:     AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAG                         GTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
genomic: AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
EST: gi|211488137|gb|FL062514.1|FL062514
EST:     GATTCTTTATGGTGAACGGTGCTTTGGATCAATATCTATCCCATATAAAG                         GTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
genomic: GATTCTTTATGGTGA-CGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
EST: gi|211488133|gb|FL062510.1|FL062510
EST:     AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAG                         GTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
genomic: AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
EST: gi|110208747|gb|EC890644.1|EC890644
EST:     AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAG                         GTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
genomic: AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
EST: gi|211488135|gb|FL062512.1|FL062512
EST:     AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAG                         GTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA
genomic: AGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCA

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 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 85

TGTAGATGAAGATGCAGTAGGATCAGTGGACCAACCTGGCTATGGAGCCAAGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCACCATCCCGAGCCATTGGCATGTGATTCCTGGCTCTGACCGCACTAGTGT


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 42

TGTAGATGAAGATGCAGTAGGATCAGTGGACCAACCTGGCTATGGAGCCAAGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCACCATCCCGAGCCATTGGCATGTGATTCCTGGCTCTGACCGCACTAGTGT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 43

TGTAGATGAAGATGCAGTAGGATCAGTGGACCAACCTGGCTATGGAGCCAAGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCACCATCCCGAGCCATTGGCATGTGATTCCTGGCTCTGACCGCACTAGTGT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 52

TGTAGATGAAGATGCAGTAGGATCAGTGGACCAACCTGGCTATGGAGCCAAGATTCTTTATGGTGACGGTGCTTTGGATCAATATCTATCCCATATAAAGgtaaatctta ... attgtgacagGTGGCGGGAGATGGAGTCGCAAGCGAAATGGATGGAGAAGCTGAGCTTTCACCATCCCGAGCCATTGGCATGTGATTCCTGGCTCTGACCGCACTAGTGT