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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaaatgctttgcttctagtttacctgtcttgtaactgtgcattctaatataaactgaatatacatacttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCTGTGAGGCCTAGAGTGCTTTTAGCGCCCGCACAGTGGCAG

Basic information

species Zea mays
transcript GRMZM2G031435_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031435_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g44910.1 (Oryza sativa), 3'ss of exon 4
------------gtaagaaaaatgctttgcttctagtttacctgtcttgtaactgtgcattctaatataaactgaatatacatacttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCTGTGAGGCCTAGAGTGCTTTTAGCGCCCGCACAGTGGCAG
            | |  ||  |||   || || | || | | |   || ||  |||    | || |   | || |   |   |      ||||||| |||||||| || |||||||||||||  ||||| ||||||||  ||||||| ||||| ||||| |||||||| ||  | || ||||||
gtatgagaaactgcattaatcatgtgatgtttattgtatgcattatttttatttgtttcatata-tggcatcttatctttggtgtaacttgcagATTAAGTACAGGAACATGACTCCTGAAGCTGCTTTAGATCATGCACGGTCTGTAAGGCCCAGAGTACTTTTAGCACCATCTCAATGGCAG
















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|93284231|gb|EB676495.1|EB676495
EST:     ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTG                         ATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
genomic: ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
EST: gi|71448351|gb|DR829401.1|DR829401
EST:     ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTG                         ATCAAGTACAGAAATATGACTCCCTGA-GTAGCTTTGGATCAT
genomic: ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCC-TGAAGTAGCTTTGGATCAT
EST: gi|71439137|gb|DR820187.1|DR820187
EST:     CTGGTA-GGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTG                         ATNCA-GTACAGAAATATGACTCCTGAAGTA
genomic: CTG-TAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagAT-CAAGTACAGAAATATGACTCCTGAAGTA
EST: gi|71766612|gb|DR964549.1|DR964549
EST:     ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGGGTTTTTTG                         ATCAAGAACAGAAATATGA
genomic: ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGA
EST: gi|19057494|gb|BM736161.1|BM736161
EST:     ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTG                         ATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
genomic: ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
EST: gi|78103952|gb|DV522370.1|DV522370
EST:     ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTG                         ATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
genomic: ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
EST: gi|71430075|gb|DR811125.1|DR811125
EST:     ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTG                         ATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
genomic: ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
EST: gi|76288945|gb|DV028513.1|DV028513
EST:     ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTG                         ATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
genomic: ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
EST: gi|76280780|gb|DV020348.1|DV020348
EST:     ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTG                         ATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
genomic: ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
EST: gi|87152319|gb|DY397108.1|DY397108
EST:     ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTG                         ATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
genomic: ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
EST: gi|74232090|gb|DT640004.1|DT640004
EST:     ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTG                         ATTCA-GTACAGAAATATGACTCCTGAAGTA-CTTTTGGATC
genomic: ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagAT-CAAGTACAGAAATATGACTCCTGAAGTAGCTTT-GGATC
EST: gi|101383931|gb|EB814020.1|EB814020
EST:     ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTG                         ATCAAGTACAGAAATATGACTCCTGAAGTACCTTTGGATCATGCGAG
genomic: ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAG
EST: gi|22491044|gb|BU050967.1|BU050967
EST:     ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTG                         ATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT
genomic: ACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCT

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: 49 (upstream exon), 47 (downstream exon)
Score: 78

GTAATGAAGTGCAAGGTGGTAGCACCTATGTCCACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCTGTGAGGCCTAGAGTGCTTTTAGCGCCCGCACAGTGGCAG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 57

GTAATGAAGTGCAAGGTGGTAGCACCTATGTCCACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCTGTGAGGCCTAGAGTGCTTTTAGCGCCCGCACAGTGGCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 80

GTAATGAAGTGCAAGGTGGTAGCACCTATGTCCACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCTGTGAGGCCTAGAGTGCTTTTAGCGCCCGCACAGTGGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 106

GTAATGAAGTGCAAGGTGGTAGCACCTATGTCCACTGTAAGGCTGGAAGGGGACGAAGCACCACTATAGTTTTGTGTTTTTTGgtaagaaaaa ... cttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCTGTGAGGCCTAGAGTGCTTTTAGCGCCCGCACAGTGGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgtcttgtaactgtgcattctaatataaactgaatatacatacttaatgcagATCAAGTACAGAAATATGACTCCTGAAGTAGCTTTGGATCATGCGAGGTCTGTGAGGCCTAGAGTGCTTTTAGCGCCCGCACAGTGGCAG
                       taatataaactgaata  TA-rich tract