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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagctattagtctattgtgtaaaatggtgacagttttattaaaaaaatattacaagtttttccttcatatggatttgtag

Basic information

species Zea mays
transcript GRMZM2G151977_T01
intron # 6
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 6
lower sequence: LOC_Os12g03190.1 (Oryza sativa), 5'ss of exon 6
GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagctattagtctatt-gtgta-aaatggtgacagtttt---attaaaaaaatattacaagtttttccttcatatggatttgtag
|||||||| ||||||||||| ||||||||||| |||||||||||||| |||||||| ||  || ||||||||||||||||| |||||||||  ||| |||||   |||| || |  ||| ||||   |||||   | ||  | |  | |  |    || | ||| ||||  | || ||
GTTGGAGCCGGTTTGCCTGTAATAGCTTCTGTGACCCGTATTATTGCCTCTGGAGATCCAGTTTCTCGTATTGTTGGCAGTCTGAGTGgtacacagttattatcttatttgtttgtaaaaggtgtttgttttccaaatagcagagcaatgtaccacttccattc-tatgattctgcag

upper sequence: GRMZM2G151977_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os11g03470.1 (Oryza sativa), 5'ss of exon 6
GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagctattagtctatt-gtgta-aaatggtgacagtttt---attaaaaaaatattacaagtttttccttcatatggatttgtag
||||||||  || ||||||| ||||||||||| || ||||||||||| |||||||| ||  || ||||||||||||||||| |||||||||  ||| ||||| | |||| || |  ||| |||| | |||||   | ||  | |  | |  |   ||  | ||| ||||  | || ||
GTTGGAGCCAGTCTGCCTGTAATAGCTTCTGTGACTCGTATTATTGCCTCTGGAGATCCAGTTTCTCGTATTGTTGGCAGTCTGAGTGgtacacagttattattttatttgtttgtaaaaggtgtctgttttccaaatagcagagcaatgtacacttc-cattcctatgattctgcag
















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:     TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG                         GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
genomic: TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagct ... ggatttgtagGTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
EST: gi|148952245|gb|EC898050.2|EC898050
EST:     TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG                         GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAA-AAATTTAGTG
genomic: TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagct ... ggatttgtagGTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
EST: gi|78080728|gb|DV509140.1|DV509140
EST:     TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG                         GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
genomic: TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagct ... ggatttgtagGTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
EST: gi|148966141|gb|EE017084.2|EE017084
EST:     TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG                         GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
genomic: TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagct ... ggatttgtagGTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
EST: gi|148944776|gb|EC889918.2|EC889918
EST:     TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG                         GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
genomic: TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagct ... ggatttgtagGTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
EST: gi|31361610|gb|CD445967.1|CD445967
EST:     TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG                         GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
genomic: TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagct ... ggatttgtagGTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
EST: gi|71770930|gb|DR968867.1|DR968867
EST:     TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG                         GTACACTTGGGTATGTGATGAGTGAGCTTGANGATGGAAAGAAATTTAGTG
genomic: TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagct ... ggatttgtagGTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
EST: gi|148936622|gb|EC880746.2|EC880746
EST:     TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG                         GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
genomic: TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagct ... ggatttgtagGTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
EST: gi|40334075|gb|CK368145.1|CK368145
EST:     TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTG                         GTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG
genomic: TATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagct ... ggatttgtagGTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTG

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: 46 (upstream exon), 47 (downstream exon)
Score: 116

GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagct ... ggatttgtagGTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 114

GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagct ... ggatttgtagGTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 110

GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagct ... ggatttgtagGTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 115

GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagct ... ggatttgtagGTACACTTGGGTATGTGATGAGTGAGCTTGAGGATGGAAAGAAATTTAGTGAAGTTGTAAAAACTGCCAAGTCCCTTGGCTATACAGAACCAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGAGCAGGTTTGCCTGTGATAGCTTCTGTAACCCGTATTATTGCATCTGGAGACCCTATTACTCGTATTGTTGGCAGTTTGAGTGgtatgcagctattagtctattgtgtaaaatggtgacagttttattaaaaaaatattacaagtttttccttcatatggatttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA