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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctctttctttgaattctaaacatgagtcaacatatagtggggcatagaatgacaatttcatagggattatgctctcctttcctatgctgacat...

Basic information

species Zea mays
transcript GRMZM2G098815_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098815_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g09610.1 (Oryza sativa), 5'ss of exon 3
GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctctttctttgaattctaaacatgagtcaacatatagtggggcatagaatgacaatttcatagggattatgctctcctttcctatgctgacat---------------------------
||||||||||||||||| ||||| ||||| |||||||| ||||||||||| || ||||||||| | |||||||| | ||| |  ||||| |   || |  ||   ||   ||    | | |||  ||    ||  | | |  ||| | |||| || |    | |  | | ||  | ||||    | |                           
GCAGCCTGTGATGAAACATCAGAAAAATCGGAACGGGCATTTGTCCAACTTTTGTTGACTTCAGCAAGTGGAAACAATAACATTGAGgtgtggcctat--ctacaaacattag---taaatca-tattggttgtaggacattatggcgattttattgctcctttcatgtgctgacatatgtatgcttattttggcattggtttgtatgtctcag
















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|71438169|gb|DR819219.1|DR819219
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|78117671|gb|DV536058.1|DV536058
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|148952745|gb|EC898726.2|EC898726
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|71438316|gb|DR819366.1|DR819366
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|74245464|gb|DT653378.1|DT653378
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|71433709|gb|DR814759.1|DR814759
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|76926415|gb|DV170849.1|DV170849
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|149082609|gb|EE171808.2|EE171808
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|50336738|gb|CO531864.1|CO531864
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|89253146|gb|DY624932.1|DY624932
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|211052434|gb|FL214545.1|FL214545
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|71765717|gb|DR963654.1|DR963654
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|91873215|gb|EB403172.1|EB403172
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|149076111|gb|EE164690.2|EE164690
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|14245049|gb|BG873631.1|BG873631
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|78120056|gb|DV538440.1|DV538440
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
EST: gi|148960798|gb|EE011460.2|EE011460
EST:     CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAG                         GTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT
genomic: CGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCT

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), 46 (downstream exon)
Score: 81

GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCTCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 70

GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 57

GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctc ... tgtttctcagGTCCTGAATCAGTCTGCCCTTGATTACATAAATGGATCTGTTTCAGCATCTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGCCTGTGATGAAACGTCAGAGAAATCAGAACGGGCGTTTGTCCAACTATTATTGACTTCATCTAGTGGAAATAGTAATAACGAGgtcttttctctttctttgaattctaaacatgagtcaacatatagtggggcatagaatgacaatttcatagggattatgctctcctttcctatgctgacat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA