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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggttgatacttatgcttacactttttgactgaccattttgattctgtgaagctaactgtgtggttttctattttttaaacttactggag

Basic information

species Zea mays
transcript GRMZM2G070113_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070113_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os05g36120.1 (Oryza sativa), 5'ss of exon 10
AGATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggttg-----atacttatgctta------cactttttgactgaccattttgattctgtgaagctaactgtgtggttttctattttttaaacttactggag---
||||||||||| |||||||| ||||||||||| || || ||||||||||||||| | | || | ||| | ||| ||||| || || | || | || |||| |||| | |||| | | ||| ||| ||| || ||
GGATTTCACAAACCCATCATTGCCTACAGAACAGCGTCCAAGGGCCTCTCAGgttagagtgtgcttatgttctttttgttatcacatcacttgtttcatggacccatttttgctctgaaactaaatagagaattttat-tatttgaaaattattgaagcag

upper sequence: GRMZM2G070113_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os05g36120.2 (Oryza sativa), 5'ss of exon 10
AGATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggttg-----atacttatgctta------cactttttgactgaccattttgattctgtgaagctaactgtgtggttttctattttttaaacttactggag
||||||||||| |||||||| ||||||||||| || || ||||||||||||||| | | || | ||| | ||| ||||| || || | || | || |||| |||| | |||| | | ||| ||| ||| || ||
GGATTTCACAAACCCATCATTGCCTACAGAACAGCGTCCAAGGGCCTCTCAGgttagagtgtgcttatgttctttttgttatcacatcacttgtttcatggacccatttttgctctgaaactaaatagagaattttat-tatttgaaaattattgaag
















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|67016395|gb|CO445144.1|CO445144
EST:     ATTTCACAAATCCATCATTACCTACAGAACAACGTCCTAGGGCCTCT---                         CAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
genomic: ATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
EST: gi|31628085|gb|CD526434.1|CD526434
EST:     ATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAG                         CA--A-GCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
genomic: ATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
EST: gi|211376275|gb|FL144037.1|FL144037
EST:     CCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAG                         CAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
genomic: CCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
EST: gi|30031872|gb|CB833723.1|CB833723
EST:     ATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCT---                         CAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
genomic: ATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
EST: gi|61118021|gb|DN558982.1|DN558982
EST:     ATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAG                         CA--A-GCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
genomic: ATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
EST: gi|211376276|gb|FL144038.1|FL144038
EST:     CCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAG                         CAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
genomic: CCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
EST: gi|33093651|gb|CF053645.1|CF053645
EST:     ATTTCACAAATCCATCATTACCTACAGAACAACGTCCTAGGGCCTCT---                         CAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
genomic: ATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
EST: gi|71436418|gb|DR817468.1|DR817468
EST:     ATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAG                         CA--A-GCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
genomic: ATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
EST: gi|76011812|gb|DT938982.1|DT938982
EST:     ATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAG                         CA--A-GCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
genomic: ATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
EST: gi|32915229|gb|CF020041.1|CF020041
EST:     ATTTCACAAATCCATCATTACCTACAGAACAACGTCCTAGGGCCTCT---                         CAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA
genomic: ATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGA

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), 38 (downstream exon)
Score: 20

AGATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGAG


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 12

AGATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 18

AGATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGAG


Block sizes: 49 (upstream exon), 19 (downstream exon)
Score: 21

AGATTTCACAAATCCATCATTACCTACAGAACAACGCCCTAGGGCCTCTCAGgttggtggtt ... cttactggagCAGCAAGCTTATCCTGATCCAGCTAATCTCTATGCCTTCCAACAAGCTGGAG