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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctgctggtttatctttcatttgagaatattgttccactgagttcattcttgaggctgttcaatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGGTAGTCCAGGAGAAGAAGGTGTTAGAGGTTCATGTGGAGAAAGGAATGCA

Basic information

species Zea mays
transcript GRMZM2G118731_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 5
gtatgctgctggtttatctttcatttgagaatattgttccactgagttcattcttgaggctgttcaatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGGTAGTCCAGGAGAAGAAGGTGTTAGAGGTTCATGTGGAGAAAGGAATGCA
||||||   || | |||||| |||| ||  | ||  |     ||||||    ||   |  |  |   |||  ||||||||| |||||||||||||| |||||||| || ||||| |||||||| ||||||||| |||||||||| || ||||||||||| ||||| ||||||||
gtatgccattgttgtatctt-cattagaagacatcttctggttgagtttgc-ctaatgattaatt--tgtccagGTGAGATGATAAGTGACAAGGATAAATGCCCGAGTTGTAAGGGAAACAAAGTAGTCCAGCAGAAGAAGGTCTTGGAGGTTCATGTTGAGAAGGGAATGCA
















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|76293182|gb|DV032750.1|DV032750
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAG                         GTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGG
EST: gi|18964087|gb|BM660802.1|BM660802
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAG                         GTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGG
EST: gi|6095397|gb|AW120064.1|AW120064
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAG                         GTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGG
EST: gi|18963673|gb|BM660567.1|BM660567
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAG                         GTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGG
EST: gi|148964320|gb|EC905716.2|EC905716
EST:     GGCATGATCCAACAGATGAACACTGTTTTGCC-TGAATGCAAAGGATCAG                         GTGAGATCATAAGTGACAGGGACAAATGCCCAAG
genomic: GGCATGATCCAACAGATGAACACTGTTT-GCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAG
EST: gi|31348685|gb|CD433042.1|CD433042
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAG                         GTGAGATCATAAGTGACAAGGACAAATGCCCAAGCT
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCT
EST: gi|32930958|gb|CF035770.1|CF035770
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAG                         GTGAGATCATAAGTGACAAGGACAAATGCCCAAGTTGTAAAGGAAACAAGG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGG
EST: gi|148931484|gb|EC874496.2|EC874496
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAG                         GTGAGATCATAAGTGACAAGGACAAATGCCCAAGCT
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCT
EST: gi|148955629|gb|EC901294.2|EC901294
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAG                         GTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGG
EST: gi|13150523|gb|BG320845.1|BG320845
EST:     TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAG                         GTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGRAACAAGG
genomic: TGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGG

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: 294

CATGGTTGTCGTGGTGCTGGAATGAGAACAATCACAAGACAGATAGGCCTTGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGGTAGTCCAGGAGAAGAAGGTGTTAGAGGTTCATGTGGAGAAAGGAATGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 325

CATGGTTGTCGTGGTGCTGGAATGAGAACAATCACAAGACAGATAGGCCTTGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGGTAGTCCAGGAGAAGAAGGTGTTAGAGGTTCATGTGGAGAAAGGAATGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 327

CATGGTTGTCGTGGTGCTGGAATGAGAACAATCACAAGACAGATAGGCCTTGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGGTAGTCCAGGAGAAGAAGGTGTTAGAGGTTCATGTGGAGAAAGGAATGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 353

CATGGTTGTCGTGGTGCTGGAATGAGAACAATCACAAGACAGATAGGCCTTGGCATGATCCAACAGATGAACACTGTTTGCCCTGAATGCAAAGGATCAGgtatgctgct ... caatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGGTAGTCCAGGAGAAGAAGGTGTTAGAGGTTCATGTGGAGAAAGGAATGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttgagaatattgttccactgagttcattcttgaggctgttcaatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGGTAGTCCAGGAGAAGAAGGTGTTAGAGGTTCATGTGGAGAAAGGAATGCA
          aatattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctgctggtttatctttcatttgagaatattgttccactgagttcattcttgaggctgttcaatgtttagGTGAGATCATAAGTGACAAGGACAAATGCCCAAGCTGTAAAGGAAACAAGGTAGTCCAGGAGAAGAAGGTGTTAGAGGTTCATGTGGAGAAAGGAATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA