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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctctttctctttatggctaatagccaatttgaaataatactagatgagggtcctcgaatggcgactgatttcaactttcctgaactgcag

Basic information

species Zea mays
transcript GRMZM2G040017_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040017_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g55940.1 (Oryza sativa), 5'ss of exon 4
GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctctttctctttatggctaatagccaatttgaaataatactagatgagggtcctcgaatggcgactgatttcaactttcctgaactgcag
|||||| |||||||||||||||||||||||||||| | ||| | ||||||  | ||| || |||  |||  ||     |  || |  |   |||  |      ||||   |       | |||||
GCAGCTCGCAATATACACTGGTCCAACAGgtatgcatttttatttttatgatttataacctattacaaa--atggagaaccagtgaac---aataacagacattttcttttaataccgattgcag
















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|71769706|gb|DR967643.1|DR967643
EST:     GCAGCTTGCAATATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
genomic: GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
EST: gi|149075133|gb|EE163627.2|EE163627
EST:     GCAGCTTGCAATATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
genomic: GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
EST: gi|149072532|gb|EE160814.2|EE160814
EST:     GCAGCTTGCAATATACACTGGTTCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
genomic: GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
EST: gi|89760510|gb|DY688889.1|DY688889
EST:     GCAGCTTGCAATATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
genomic: GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
EST: gi|60339318|gb|DN206291.1|DN206291
EST:     GCAGCTTGCAATATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
genomic: GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
EST: gi|149085154|gb|EE174658.2|EE174658
EST:     GCAGCTTGCAATATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG
genomic: GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTG

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), 49 (downstream exon)
Score: 51

GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 108

GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 89

GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT


Block sizes: 29 (upstream exon), 49 (downstream exon)
Score: 135

GCAGCTTGCAATATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT