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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAGTTGTTAATGATACTTTAGGGGCCTGTGGTGACCTGCCTGGAGAGCAACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAGgtaaaaccagagccacattttaaacacatgagaaatatttgtttcactaaaaggcaagtaataatctgtcattcttttttttacag

Basic information

species Zea mays
transcript GRMZM2G037624_T03
intron # 10
splice site 5'
intron type U2

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|60398284|gb|DN231100.1|DN231100
EST:     AACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAG                         AAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATC
genomic: AACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAGgtaaaaccag ... ttttttacagAAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATC
EST: gi|149009603|gb|EE154023.2|EE154023
EST:     AACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAG                         AAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATC
genomic: AACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAGgtaaaaccag ... ttttttacagAAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATC
EST: gi|149056982|gb|EE156538.2|EE156538
EST:     AACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAG                         AAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATC
genomic: AACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAGgtaaaaccag ... ttttttacagAAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATC
EST: gi|71450153|gb|DR831203.1|DR831203
EST:     AACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAG                         AAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATC
genomic: AACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAGgtaaaaccag ... ttttttacagAAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATC
EST: gi|78025068|gb|DV493455.1|DV493455
EST:     TGGCAATGCGGTTAAACCAAG                         AAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATC
genomic: TGGCAATGCGGTTATACCAAGgtaaaaccag ... ttttttacagAAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATC
EST: gi|91869810|gb|EB400552.1|EB400552
EST:     AACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAG                         AAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATC
genomic: AACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAGgtaaaaccag ... ttttttacagAAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATC
EST: gi|91056761|gb|EB167179.1|EB167179
EST:     AACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAG                         AAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTTTGAGCCTATC
genomic: AACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAGgtaaaaccag ... ttttttacagAAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATC

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), 47 (downstream exon)
Score: 57

CTCAGTTGTTAATGATACTTTAGGGGCCTGTGGTGACCTGCCTGGAGAGCAACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAGgtaaaaccag ... ttttttacagAAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 41

CTCAGTTGTTAATGATACTTTAGGGGCCTGTGGTGACCTGCCTGGAGAGCAACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAGgtaaaaccag ... ttttttacagAAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 40

CTCAGTTGTTAATGATACTTTAGGGGCCTGTGGTGACCTGCCTGGAGAGCAACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAGgtaaaaccag ... ttttttacagAAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAG


Block sizes: 41 (upstream exon), 46 (downstream exon)
Score: 31

CTCAGTTGTTAATGATACTTTAGGGGCCTGTGGTGACCTGCCTGGAGAGCAACAAGGCCCTTGCCTACCTTATTATGTGTGGCAATGCGGTTATACCAAGgtaaaaccag ... ttttttacagAAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAG