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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttcgcattcttcttaccttgtattttttatttattctacacctaacgttatcccatgttgttcttgaaatggttgttgatctactgtcggcat...

Basic information

species Zea mays
transcript GRMZM2G158097_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158097_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g36062.1 (Oryza sativa), 5'ss of exon 9
AGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggt-----ttcgcattcttcttaccttgtattttttatttattctacacctaacgttatcccatgttgttcttgaaatggttgttgatctactgtcggcat
|||   || ||||||||||| ||||| |||||||| ||||||||||||||||||||  ||     | |   |  || |||   |||| |  ||   |||     |  |    |||| |||| |  |    |    |  | ||  ||||   | | |  
AGCGAGCATTGGGACACCTTTTATAAGTTCTACCGCAACACAACTGATAATCAgttcagtgcatttccttgtaatttttaaaatgtactaattccctatgtgcaaattggaattataccatataatgtgggcgtcg--tattagtctaaaat-gac--
















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|71766886|gb|DR964823.1|DR964823
EST:     CTTCTATAAATTCTACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: CTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
EST: gi|78124181|gb|DV542565.1|DV542565
EST:     ACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: ACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
EST: gi|32841147|gb|CD980828.1|CD980828
EST:     AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
EST: gi|32840869|gb|CD980550.1|CD980550
EST:     AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
EST: gi|13389377|gb|BG462692.1|BG462692
EST:     AGATTTTTTGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
EST: gi|32841581|gb|CD981262.1|CD981262
EST:     AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
EST: gi|32841639|gb|CD981320.1|CD981320
EST:     AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA

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: 47 (upstream exon), 49 (downstream exon)
Score: 34

AGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAAGATGGGGGATAATGTGATGCTTATAGTTGCTGAAAAAGATGATAAACTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 55

AGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAAGATGGGGGATAATGTGATGCTTATAGTTGCTGAAAAAGATGATAAACTA


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 35

AGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAAGATGGGGGATAATGTGATGCTTATAGTTGCTGAAAAAGATGATAAACTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 46

AGCAGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAAGATGGGGGATAATGTGATGCTTATAGTTGCTGAAAAAGATGATAAACTA