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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgtgaaatggtcataatctcatagaaatcatgaaaggttcatcttttccccttactttcgtagaacaaatcgcggatttgaaaacgaactaatccagggtgtctttgatctgtgtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG

Basic information

species Zea mays
transcript GRMZM2G173321_T02
intron # 2
splice site 3'
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|211138903|gb|FL206376.1|FL206376
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|26456740|gb|CA828323.1|CA828323
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|76936192|gb|DV174627.1|DV174627
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|78074656|gb|DV503090.1|DV503090
EST:     GCCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|149051910|gb|EE156043.2|EE156043
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|78093455|gb|DV521829.1|DV521829
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|26457345|gb|CA828928.1|CA828928
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|211138901|gb|FL206374.1|FL206374
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|71333334|gb|DR803728.1|DR803728
EST:     CCGATAAGTCCGTGCACCGCGAGG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: CCGATAAGTCCGTGCACCGCGA-Ggtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|60397540|gb|DN230356.1|DN230356
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|93281470|gb|EB673734.1|EB673734
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|211138904|gb|FL206377.1|FL206377
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|211138900|gb|FL206373.1|FL206373
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|211139833|gb|FL206379.1|FL206379
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|211139832|gb|FL206378.1|FL206378
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|211138902|gb|FL206375.1|FL206375
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|20507484|gb|BQ279652.1|BQ279652
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
EST: gi|71333335|gb|DR803729.1|DR803729
EST:     GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAG                         GAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
genomic: GGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG

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), 48 (downstream exon)
Score: 46

GAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATGGAGCCACTACGGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG


Block sizes: 43 (upstream exon), 42 (downstream exon)
Score: 4

GAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATGGAGCCACTACGGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 11

GAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATGGAGCCACTACGGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG


Block sizes: 39 (upstream exon), 40 (downstream exon)
Score: 6

GAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATGGAGCCACTACGGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCGTGCACCGCGAGgtcagtgtga ... gtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgcggatttgaaaacgaactaatccagggtgtctttgatctgtgtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG
       atttgaaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgtgaaatggtcataatctcatagaaatcatgaaaggttcatcttttccccttactttcgtagaacaaatcgcggatttgaaaacgaactaatccagggtgtctttgatctgtgtctgtgcagGAGGTTCCAACTTTTTGGAGAAAGATTAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA