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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagagtgacatttaatgtcttactcctagtactgctcctaagcctcctgtgtcaatggatacactttttgtgacgtgtggctgtccatacag

Basic information

species Zea mays
transcript GRMZM2G131756_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131756_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os05g37350.1 (Oryza sativa), 5'ss of exon 17
GTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagagtgacatttaatgtcttactcctagtactgctcctaa--gcctcctgtgtcaatggatacactt---tttgtgacgtgtgg--ctgtccatacag
|||||||| |||||||| ||||| |||||||| |||||||||||||||||||||||||| |||||||||  | |||| | || |       ||    ||| |  |     |   ||   |  ||    |  ||| | ||   |||  ||  | |||   |||   | |||
GTTCCTTGCCGAACAGCCATGAGAGGTAGTTTTCCACTTAATGGCACTTACTTTCAAGTTAATGAGgtatgctgagttatatctgtcaaagtatgagtaggatagtggagagttgctatccatgggcctttatagagttgactttacgatttctggatttgtttttgcag

upper sequence: GRMZM2G131756_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os05g37410.1 (Oryza sativa), 5'ss of exon 18
GTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagagtgacatttaatgtcttactcctagtactgc------tcctaagcctcctgtgtcaatggatacactttttgtgacgtgtgg--ctgtccatacag
|||||||| |||||||| ||||| |||||||| |||||||||||||||||||||||||| |||||||||  | |||| | || |       ||    ||| |  |       |    | ||    |  |  || ||       |||  ||  | |||   |||   | |||
GTTCCTTGCCGAACAGCCATGAGAGGTAGTTTTCCACTTAATGGCACTTACTTTCAAGTTAATGAGgtatgctgagttatatctgtcaaagtatgagtaggatagtggagagttgctatccatgggcctttatagagttggactttacgatttctggatttgtttttgcag
















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|211540330|gb|FL320588.1|FL320588
EST:     CTATGAGGGGTAGTTTCCCACTTAACGGCACTTACTTTCAAGTCAATGAG                         GTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
genomic: CTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagag ... gtccatacagGTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
EST: gi|211151599|gb|FL276380.1|FL276380
EST:     CTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAG                         GTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
genomic: CTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagag ... gtccatacagGTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
EST: gi|60339031|gb|DN206004.1|DN206004
EST:     CTATGAGGGGTAGTTTCCCACTTAACGGCACTTACTTTCAAGTCAATGAG                         GTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
genomic: CTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagag ... gtccatacagGTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
EST: gi|60347567|gb|DN214540.1|DN214540
EST:     CTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAG                         GTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
genomic: CTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagag ... gtccatacagGTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
EST: gi|60394289|gb|DN227159.1|DN227159
EST:     CTTAACGGCACTTACTTTCAAGTCAATGAG                         GTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
genomic: CTTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagag ... gtccatacagGTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
EST: gi|9731007|gb|BE509759.1|BE509759
EST:     TTAATGGCACTTACTTTCAAGTCAATGAG                         GTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
genomic: TTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagag ... gtccatacagGTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
EST: gi|5901234|gb|AW042334.1|AW042334
EST:     CTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAG                         GTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
genomic: CTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagag ... gtccatacagGTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAG
EST: gi|60353813|gb|DN220786.1|DN220786
EST:     GAGGGGTAGTTTCCCCACTTAATGGCACTTACTTTCAAGTCAATGAAG                         GTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGA
genomic: GAGGGGTAGTTT-CCCACTTAATGGCACTTACTTTCAAGTCAATG-AGgtaaacagag ... gtccatacagGTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGA

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: 697

GTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagag ... gtccatacagGTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAGATGCTATGGAACTTGCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 50

GTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagag ... gtccatacagGTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAGATGCTATGGAACTTGCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

GTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagag ... gtccatacagGTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAGATGCTATGGAACTTGCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 142

GTTCCTTGTCGAACAGCTATGAGGGGTAGTTTCCCACTTAATGGCACTTACTTTCAAGTCAATGAGgtaaacagag ... gtccatacagGTATTTGCTGACCACAGATCTAGCCACAACCCAATCCATGTGGAAAGGGAGATGCTATGGAACTTGCAAAGGCGCATGGTCTTTTTCGGGACTTCAGTAC