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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatactgtcacatttaaatatctgctcatagattttctttcttcttaagaaatagcttttactttctgactaaccaatattaatcttgtag

Basic information

species Zea mays
transcript GRMZM2G174757_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 5'ss of exon 6
GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatactgtc--acatttaaatatctgctcatagattttctttctt-cttaagaaatagcttttactttctgactaaccaatattaatcttgtag
|||||||||||||||||||| ||||||||||  |||||||||||||| || ||||| ||||||||||||||||||||||| ||||||||  || |||  ||||| |  ||||||||||||| ||| | ||||  |||  |   | | | ||                               
GTGAAACTGATTGACTTCTCCCCTGGTGAGAAATATTTGGTCACATATAGTAGCCACGAGCCCAGCAACCCTAGAGACACTCATgtaagggaccgtcttacattcatttatctgctcatagctttcccttctgacttttgtgctggatgttgtag---------------------------

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA07G14870.1 (Glycine max), 5'ss of exon 6
GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatactgtcacatttaaatatctgctcatagattttctttcttcttaagaaatagcttttactttctgactaaccaatattaatcttgtag
|| ||||| ||||| || || |||||||||| ||||||||| ||||| ||||||||||| || ||||| ||  ||||  |  |||| || | || |    |||   | | |  | ||||  |||    | | |||   |    || || ||  | ||||      |     |  |||||
GTAAAACTTATTGATTTTTCGCCTGGTGAGAAGTATTTGGTAACATATAGCAGCCATGAACCAAGCAATCCCCGAGATGCCAATgtgag-tgcttttttctttgtttttattttaatagtattttagacattttagaca----ctgttcctaacagactctttttttccctttctgtag

upper sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv04s0008g07070.t01 (Vitis vinifera), 5'ss of exon 6
GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatactgtcac-atttaaatatctgctcatagattttctttcttcttaagaaatagcttttactttctgactaaccaatattaatcttgtag
|| ||||||||||| ||||| |||||||||| ||||||||| || |||||||||||||| || ||||| ||| | || || ||||| || |  |   || ||     ||  |  |  | | ||   |||    |  ||  ||  ||  |     ||    |   |               
GTTAAACTGATTGATTTCTCCCCTGGTGAGAAGTATTTGGTTACCTACAGCAGCCATGAACCAAGCAATCCTCGCGATACTCATgtgagttttttctactatgcctttaattcgttgttggttaattttggcttagagccatgtctaatgtgagctcttgatgtag--------------

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|31351129|gb|CD435486.1|CD435486
EST:     ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT                         AGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
genomic: ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatact ... aatcttgtagAGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
EST: gi|22546320|gb|BU098631.1|BU098631
EST:     ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT                         AGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
genomic: ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatact ... aatcttgtagAGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
EST: gi|22521176|gb|BU079987.1|BU079987
EST:     ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT                         AGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
genomic: ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatact ... aatcttgtagAGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
EST: gi|22472476|gb|BU036956.1|BU036956
EST:     CCAGCAACCCTAGAGACACACAT                         AGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
genomic: CCAGCAACCCTAGAGACACACATgtaagatact ... aatcttgtagAGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
EST: gi|22542190|gb|BU092628.1|BU092628
EST:     ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT                         AGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
genomic: ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatact ... aatcttgtagAGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
EST: gi|32841675|gb|CD981356.1|CD981356
EST:     ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT                         AGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
genomic: ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatact ... aatcttgtagAGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
EST: gi|32841369|gb|CD981050.1|CD981050
EST:     ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT                         AGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
genomic: ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatact ... aatcttgtagAGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
EST: gi|60350764|gb|DN217737.1|DN217737
EST:     ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT                         AGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
genomic: ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatact ... aatcttgtagAGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
EST: gi|32841679|gb|CD981360.1|CD981360
EST:     ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACAT                         AGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC
genomic: ATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatact ... aatcttgtagAGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGAC

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: 46 (upstream exon), 49 (downstream exon)
Score: 992

GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatact ... aatcttgtagAGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGACTTTAAGGGAAGCGCTGATGATTTTACTACTGGCGGGAATATTGGGGTTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 671

GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatact ... aatcttgtagAGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGACTTTAAGGGAAGCGCTGATGATTTTACTACTGGCGGGAATATTGGGGTTT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 475

GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatact ... aatcttgtagAGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGACTTTAAGGGAAGCGCTGATGATTTTACTACTGGCGGGAATATTGGGGTTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 864

GTGAAACTGATTGACTTCTCTCCTGGTGAGAGGTATTTGGTCACATACAGCAGCCATGAGCCCAGCAACCCTAGAGACACACATgtaagatact ... aatcttgtagAGAGTTGTCCTGAATATATTTGATGTAAGGACTGGGAAAGTGATGCGAGACTTTAAGGGAAGCGCTGATGATTTTACTACTGGCGGGAATATTGGGGTTT