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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcagatatcttttgatatatttttattacagttagtatatgtgccaatttctagtagatcttctttgtgaagtagagctcaaacaaaagtctctatgaatttgaataatctaaggtcaaggaacacatccataatatttactcctttacctgtttgcaatatgtatttattgaagtgtttttgtttgccag

Basic information

species Zea mays
transcript GRMZM2G151977_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151977_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os11g03470.1 (Oryza sativa), 5'ss of exon 7
GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcagatatcttttgatatatttt-tattacagttagtatatgtgc-caatttctagtagatcttctttgtgaagtagagctcaaacaaaagtctctatgaatttgaataatctaaggtcaaggaacacatccataatatttactcctttacctgtttgcaatatgtatttattgaagtgtttttgtttgccag
|||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||| |   | | || | || ||  |||    |||| |      || ||| | || | |  | |    ||| | |||             ||  | ||  |  ||  ||||     | | || ||| |   |  | |     |  |  |||   | |  ||||     |  |||                          
GTACACTTGGTTATGTGATGAGTGAGCTGGAGGATGGAAAGAAATTTAGTGAAGTTGTGAAAACTGCCAAGTCTCTTGGCTATACAGAACCAGgtct---aaaaatttattcattcattggacattataacatcaatgtgtactcagtattcaatt--ccttatctgt-------------aattacagatttcat--attt-----accgaaagtctactgatgcttgtgataagtgcacttactcagttgttcaattttggtag-------------------------

upper sequence: GRMZM2G151977_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g03190.1 (Oryza sativa), 5'ss of exon 7
GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcagatatcttttgatatatttt-tattacagttagtatatgtgccaatttctagtagatcttctttgtgaagtagagctcaaacaaaagtctctatgaatttgaataatctaaggtcaaggaacacatccataatatttactcctttacctgtttgcaatatgtatttattgaagtgtttttgtttgccag
|||||||||| ||||||||||||||||| ||||||||||||| ||||||||||||||| |||||||||||||| ||||||||||||||||||||| |   | | || | || ||  ||||   |||| |      || ||| |        ||||    ||| || |         ||  ||  | ||  |  |||  |    | | ||||      | |         |    | ||||||  ||   |  ||    ||                              
GTACACTTGGTTATGTGATGAGTGAGCTGGAGGATGGAAAGAGATTTAGTGAAGTTGTGAAAACTGCCAAGTCTCTTGGCTATACAGAACCAGgtct---aaaaatttattcattcatttgacattataacatcaatgtgtact------cagtattcattccttat---------ctgtaattacagatttcatgtttacagaaagtcta---ctgatgcttgtgataagtgcacttactcagttgtttaattttggtag-----------------------------
















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|32916159|gb|CF020971.1|CF020971
EST:     ATTTAGTGAAGTTGTAAAAACTGCCAAGTCTCTTGGCTATACAGAACCAG                         ATCCACGTGATGATCTTGGTGGAATGGATGT
genomic: ATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcaga ... tgtttgccagATCCACGTGATGATCTAGGTGGAATGGATGT
EST: gi|78080728|gb|DV509140.1|DV509140
EST:     ATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAAACAG                         ATCCACGTGATGATCTAG
genomic: ATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcaga ... tgtttgccagATCCACGTGATGATCTAG
EST: gi|148966141|gb|EE017084.2|EE017084
EST:     ATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAG                         AATCCACGTGATGATCTAG
genomic: ATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcaga ... tgtttgccagA-TCCACGTGATGATCTAG
EST: gi|148944776|gb|EC889918.2|EC889918
EST:     ATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAG                         ATCCACGTGATGATCTAGGTGGGATGGATGTCGCTAGAAAG
genomic: ATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcaga ... tgtttgccagATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAG
EST: gi|31361610|gb|CD445967.1|CD445967
EST:     ATTTAGTGAAGTTGTAAAAACTGCCAAGTCTCTTGGCTATACAGAACCAG                         ATCCACGTGATGATCTTGGTGGAATGGATGTGGCTAGAAAG
genomic: ATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcaga ... tgtttgccagATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAG
EST: gi|148936622|gb|EC880746.2|EC880746
EST:     ATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCCTGGCTATACAGAACCAG                         ATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAAG
genomic: ATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcaga ... tgtttgccagATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAA-G
EST: gi|40334075|gb|CK368145.1|CK368145
EST:     ATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAG                         ATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAG
genomic: ATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcaga ... tgtttgccagATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAG

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: 48 (upstream exon), 40 (downstream exon)
Score: 50

GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcaga ... tgtttgccagATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 79

GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcaga ... tgtttgccagATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 55

GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcaga ... tgtttgccagATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAG


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 48

GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAGgtattgcaga ... tgtttgccagATCCACGTGATGATCTAGGTGGAATGGATGTCGCTAGAAAG