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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcaggatcgtaggattaaacctatttgttgtgctgtctatgctgcgctatatgttacgactaagtgtctctgttcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTACTGGGTGGAGCTTTCTTCGTGGCTGGAAATGTCAACCCTGCTGCTGAAG

Basic information

species Zea mays
transcript GRMZM2G085960_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085960_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g44370.1 (Oryza sativa), 3'ss of exon 4
gtatgttcaggatcgtaggattaaacctatttgttgtgctgtct---atgctgcgctatatgttacgactaagtgtctctgttcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTACTGGGTGGAGCTTTCTTCGTGGCTGGAAATGTCAACCCTGCTGCTGAAG
||||| |     |   ||||| |||||| |||    || ||  |   |||| | |  | | | || | ||    |||| ||||||| |||||||||||||| | ||||||||||||||||| |||||||| |||||||||||||||||||| |||||||| | |||||||||||||| ||| ||||||||||
gtatgcttccatttacaggat-aaacctgtttagcatgttgctttatatgccgtgacagaggataagtct----gtctgtgttctttcttagGCCATCAAAAGGGACCCTTCCTTTGCAAGTAAGGTGAAGAAAATAGTTGTACTGGGTGGTGCTTTCTTTGCGGCTGGAAATGTCAGCCCAGCTGCTGAAG

upper sequence: GRMZM2G085960_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G36310.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgttcaggatcgtaggattaaacctatttgttgtgctgtctatgctgcgctatatgttacgactaagtgtctctgttcttgct-tagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTACTGGGTGGAGCTTTCTTCGTGGCTGGAAATGTCAACCCTGCTGCTGAAG
      | || ||| |      || ||  |   ||   ||   ||   | || | | |||   ||| | |      | || | | | |||||||||||||| ||   ||| ||||| ||||||||||| ||||| ||| | || ||||||||||||||       ||||||||||| ||||| ||||| |
-----gtaagaatcatg-----aatcccctcctttaatcttcttaaaatccgatttgtgtactgacgatgaccgggttttttcgttatagGCCATCAAACGCGATAGTTCATTTGCGAGCAAGGTGAAGAAAATTGTTATTCTTGGTGGAGCTTTCTTTTCTTTGGGAAATGTCAATCCTGCAGCTGAGG
















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|74241088|gb|DT649002.1|DT649002
EST:     CAAGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAACGAGACCCTTCCTTTGCCAA-CAAGGTGAATAAAATAGTTGT
genomic: CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTTGC-AAGCAAGGTGAATAAAATAGTTGT
EST: gi|93013944|gb|EB639464.1|EB639464
EST:     CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAACGAGACCCCTTCCTTTGCAAGCCAGGTGAATAAAAATACTTG
genomic: CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCC-TTCCTTTGCAAGCAAGGTGAATAAAA-TAGTTG
EST: gi|78105353|gb|DV523771.1|DV523771
EST:     CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTA
EST: gi|78103961|gb|DV522379.1|DV522379
EST:     CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGGGA-TAAAATAGTT
genomic: CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTT
EST: gi|71448364|gb|DR829414.1|DR829414
EST:     CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTA
EST: gi|91048127|gb|EB158545.1|EB158545
EST:     CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAACGAGACCCTTCCTTTTGCA-GCAAGGTGAATAAAATAGTTGT
genomic: CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTT-GCAAGCAAGGTGAATAAAATAGTTGT
EST: gi|74238611|gb|DT646525.1|DT646525
EST:     CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTA
EST: gi|149058761|gb|EE156779.2|EE156779
EST:     CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTA
EST: gi|16925487|gb|BM078555.1|BM078555
EST:     CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTG                         GCCATTAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAAT
genomic: CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAAT
EST: gi|71432393|gb|DR813443.1|DR813443
EST:     CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTA
EST: gi|78104295|gb|DV522713.1|DV522713
EST:     CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTG                         GCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTA
genomic: CAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTA

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), 49 (downstream exon)
Score: 65

GGTTGAGGAAAGTGCTGCTGATTTCATGGTTAATAAGGTCTCTGAGTTTCCAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTACTGGGTGGAGCTTTCTTCGTGGCTGGAAATGTCAACCCTGCTGCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

GGTTGAGGAAAGTGCTGCTGATTTCATGGTTAATAAGGTCTCTGAGTTTCCAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTACTGGGTGGAGCTTTCTTCGTGGCTGGAAATGTCAACCCTGCTGCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GGTTGAGGAAAGTGCTGCTGATTTCATGGTTAATAAGGTCTCTGAGTTTCCAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTACTGGGTGGAGCTTTCTTCGTGGCTGGAAATGTCAACCCTGCTGCTGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 159

GGTTGAGGAAAGTGCTGCTGATTTCATGGTTAATAAGGTCTCTGAGTTTCCAGGAGAGGTCTCTGTGCTTGCTTTGGGACCCCTGACAAATGTAGCATTGgtatgttcag ... tcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTACTGGGTGGAGCTTTCTTCGTGGCTGGAAATGTCAACCCTGCTGCTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgctgtctatgctgcgctatatgttacgactaagtgtctctgttcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTACTGGGTGGAGCTTTCTTCGTGGCTGGAAATGTCAACCCTGCTGCTGAAG
                                      tctctgttcttgctt  CT-rich tract
                   tatatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcaggatcgtaggattaaacctatttgttgtgctgtctatgctgcgctatatgttacgactaagtgtctctgttcttgcttagGCCATCAAACGAGACCCTTCCTTTGCAAGCAAGGTGAATAAAATAGTTGTACTGGGTGGAGCTTTCTTCGTGGCTGGAAATGTCAACCCTGCTGCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG