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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagatcttcattcctaatgcatttattctgttttacaaatttatagtcaactgtaaaggtatttgcctctttgtgccgtctgacacttaactacag

Basic information

species Zea mays
transcript GRMZM2G016184_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016184_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g46410.1 (Oryza sativa), 5'ss of exon 8
GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagatcttcattcctaatgcatttat------tctgttttacaaatttatagtcaactgtaaaggtatttgcc-tctttgtgccgtctgacacttaactacag------------------
|| ||||||||| || ||||||| || ||||| || |||||||||||||| ||| |||||||| ||| || | |||| || ||||||||||      | | || ||     || |  | |  |||| |  ||       ||| | |||  ||| |||| |   ||| |                  
GTTGCAAGGATACTTCTGTTCATTTACGTATTCTATCACATCTATTTGCACTACAGTCAGgtaataacatatccattgctgatgcatttatggactctttattctattttattgtgtttatatgtacaaatacacataatctctatgctatctaacacattcttactgttctatcttcttatgcag
















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|37375483|gb|CF624180.1|CF624180
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|211033261|gb|FL440337.1|FL440337
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|6465580|gb|AW191175.1|AW191175
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|12972667|gb|BG268096.1|BG268096
EST:     ATTTTTGTTCATGTATGTATTTTACCACATGCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: ATTTTTGTTCATGTATGTATTTTACCACAT-CTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|86474267|gb|DY240637.1|DY240637
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|12972723|gb|BG268124.1|BG268124
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|166415244|gb|EG271140.1|EG271140
EST:     ATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: ATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|6526808|gb|AW216077.1|AW216077
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|37391506|gb|CF632996.1|CF632996
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|32910942|gb|CF015754.1|CF015754
EST:     TATTTTTGTTTATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|6466756|gb|AW191416.1|AW191416
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|71760532|gb|DR958469.1|DR958469
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|60400317|gb|DN233124.1|DN233124
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|148953652|gb|EC899011.2|EC899011
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|50338097|gb|CO533223.1|CO533223
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTCCCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|6827703|gb|AW331346.1|AW331346
EST:     TTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|83279176|gb|DV943184.1|DV943184
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|211286255|gb|FL063748.1|FL063748
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTNGGGTACTACCTGACATTTGTTGTGCCATC
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTT-GGGTACTACCTGACATTTGTTGTGCCATC
EST: gi|50322745|gb|CO517871.1|CO517871
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|67030326|gb|CO459075.1|CO459075
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|76293602|gb|DV033170.1|DV033170
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
EST: gi|83278187|gb|DV942195.1|DV942195
EST:     TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAG                         ATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA
genomic: TATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCA

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), 48 (downstream exon)
Score: 212

GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCAGTGCTCTTTGTAATGAACACAATGTGGTTCATGAAGATCTTAAAAGGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 87

GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCAGTGCTCTTTGTAATGAACACAATGTGGTTCATGAAGATCTTAAAAGGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 102

GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCAGTGCTCTTTGTAATGAACACAATGTGGTTCATGAAGATCTTAAAAGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 216

GTGGCAAGGATATTTTTGTTCATGTATGTATTTTACCACATCTATTTGCATTACGGTCAGgtactaagat ... ttaactacagATAATGCAGATGCATGCCTTTGGGTACTACCTGACATTTGTTGTGCCATCAGTGCTCTTTGTAATGAACACAATGTGGTTCATGAAGATCTTAAAAGGTG