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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGTgtatgttcccaccctcaggttcccccttcctctattgaggcatgtagcaaagtttgatggccatttttttctactacag

Basic information

species Zea mays
transcript GRMZM2G044237_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044237_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g17120.2 (Oryza sativa), 5'ss of exon 9
ATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGTgtatgttcc----caccctcaggttcc--------cccttcctctattgaggcatgtagcaaagtttg-atgg---ccatttt-----tttctactacag
|||||||||||| |||| | |||||| || ||||| ||||||||||| |||||||| ||||||||||||||||||||||||||| ||||     ||  ||||  ||||        |   |||||||||||  | | |  ||| |  || |||     |||| |     ||| |  |||||
ATTGGAGGAGTGCCTATCAAAATAGGAGGAATGGCCAAAGGTTCTGGGATGATTCATCCAAATATGGCAACAATGCTTGGTgtaagttctgtatcaatctcattttccacacagtcctactcctctattgatccctttctcaaggcatgtatgagcttcattataaccctttttcttacag

upper sequence: GRMZM2G044237_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G05090.1 (Glycine max), 5'ss of exon 9
ATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGTgtatgttcccaccctcaggttcccccttcctctattgaggcatgtagcaaagtttgatggcc-atttttttctactacag
 ||||||||       | ||| | || || ||||||||||||||||||||||| |||||||||||||| || |||||||| |||||| |  ||     | |||   |||  |      | | |  |   | |||    |     |  | | ||||||  ||
GTTGGAGGAACTAGGGTCAGAGTTGGGGGAATGGCTAAAGGTTCTGGAATGATCCACCCAAATATGGCTACCATGCTTGGGgtatgt-cttacttgatgcttctttcttatttggaatatgtagatttaacagtccattccttgaactgtatctactctag

upper sequence: GRMZM2G044237_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G19450.2 (Glycine max), 5'ss of exon 10
ATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGTgtatgttcccaccctcaggttcccccttcctctattgaggcatgtagcaaagtttgatggcc-atttttttctactacag
|||||||||       | ||| | || || ||||| ||||||||||||||||| |||||||||||||| || |||||||| |||||||   ||     | |||   |||  |      |   |  |   |  ||  | |     | |||| ||||||  ||
ATTGGAGGAACTAAGGTCAGAGTTGGGGGAATGGCAAAAGGTTCTGGAATGATCCACCCAAATATGGCTACCATGCTTGGGgtatgtttt-acttgatgcttctttcttatttggaatatatagatttaactgtccgttccttgaattttatctactgtag

upper sequence: GRMZM2G044237_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv08s0040g03320.t01 (Vitis vinifera), 5'ss of exon 10
ATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGTgtatgttcccaccctc-aggttcccccttcctctattgaggcatg--tagcaaagtttgatggccatttttttctactacag
 |||||||      ||||||| | || || ||||| || |||||||| ||||| || ||||||||||| || |||||||||||  ||  |     || |  |  ||  |||  | |   |   ||   ||    | |||  ||       |  | |  | |||
GTTGGAGGGACAAATATTAGAGTTGGGGGAATGGCAAAGGGTTCTGGGATGATCCATCCAAATATGGCTACCATGCTTGGTgtgcgtctctgttttctacatgtcctgttctgcaaagtaaatattcttattccactttcttgataggactactttgttccag

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|78092275|gb|DV520649.1|DV520649
EST:     TGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGT                         GTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATC
genomic: TGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGTgtatgttccc ... tctactacagGTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATC
EST: gi|60348874|gb|DN215847.1|DN215847
EST:     TGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGT                         GTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATC
genomic: TGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGTgtatgttccc ... tctactacagGTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATC
EST: gi|76917242|gb|DV166726.1|DV166726
EST:     TGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGT                         GTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATC
genomic: TGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGTgtatgttccc ... tctactacagGTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATC

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), 49 (downstream exon)
Score: 133

ATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGTgtatgttccc ... tctactacagGTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 147

ATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGTgtatgttccc ... tctactacagGTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

ATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGTgtatgttccc ... tctactacagGTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 71

ATTGGAGGAGTGGCTATTAGAATAGGTGGGATGGCTAAAGGTTCTGGAATGATTCACCCAAATATGGCAACAATGCTTGGTgtatgttccc ... tctactacagGTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACA