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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCTGTCTATGGTGTGGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcagtacattttatatatgtgtttacacttatatttctcctgactttttccaacctatccaacaatgtgttgcttatgttttcag

Basic information

species Zea mays
transcript GRMZM5G887631_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G887631_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 5'ss of exon 16
GCTGCTGTCTATGGTGTGGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcagtacattttatatatgtgtttacactt----atatttctcc-tgactttttccaacctatccaacaatgtgttgcttatgttttcag
||||||||||||||||||||||||||||| || ||||| ||||||||||| ||||| || || ||||||||  || |  |||  | || ||   |||  | ||     || ||  || ||  ||||   |||| | |||  ||| || |||||      ||||
GCTGCTGTCTATGGTGTGGGTGTATGTGCTGAATTTGGCGGTCATGTTTTCCGCCCACTTGTTGGAGgtag--tcgggtcatgct-tacatcactttgtagtttgtagtactttaccatgcattttcaaaaccaacccactaatttggtgctttcaaaatcag

upper sequence: GRMZM5G887631_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA19G29010.1 (Glycine max), 5'ss of exon 16
GCTGCTGTCTATGGTGTGGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcagtacattttatatatgtgtttacacttatatttctcctgactttttccaacctatccaacaatgtgttgcttatgttttcag
|||||||| |||||||| ||||| ||||| |||||||||||   ||||||  |||| || || ||||||   ||  | ||| |      || || |||   |  | |    ||| ||| | |  |   | |  |  ||||| |   || | ||  |||
GCTGCTGTTTATGGTGTTGGTGTTTGTGCTGAGTTTGGTGGATCTGTTTTCAGCCCCCTTGTTGGAGgttagtt--gcacaatac---catttgcttattttgttgtcatgccttactatatatattttttggataaatgtttctgttctattg-cag

upper sequence: GRMZM5G887631_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA16G04400.1 (Glycine max), 5'ss of exon 16
GCTGCTGTCTATGGTGTGGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcagtacattttatatatgtgtttacacttatatttctcctgactttttccaacctatccaacaatgtgttgcttatgttttcag
|||||||| |||||||| ||||| ||||| |||||||||||   ||||||    || || || ||||||   ||  | ||| |      || |  |||   |  | |    ||| ||| | |  |   | |  |  ||||| |   || | ||  |||
GCTGCTGTTTATGGTGTTGGTGTTTGTGCTGAGTTTGGTGGATCTGTTTTCAAACCCCTTGTTGGAGgttagtt--gcacaatac---cattttcttattttgttgtcgtgccttactatatatattttttggataaatgtttctgttctattg-cag

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|166588613|gb|EG190282.1|EG190282
EST:     AGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACT-C
genomic: AGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|60352763|gb|DN219736.1|DN219736
EST:     GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
genomic: GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|211015404|gb|FL213618.1|FL213618
EST:     CATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
genomic: CATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|61119517|gb|DN560478.1|DN560478
EST:     GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTCATAAGGCATCCTGATGCACGACTTC
genomic: GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|33094008|gb|CF054002.1|CF054002
EST:     GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
genomic: GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|9028748|gb|BE238788.1|BE238788
EST:     GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
genomic: GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|9028539|gb|BE238534.1|BE238534
EST:     GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
genomic: GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|71770781|gb|DR968718.1|DR968718
EST:     TTTT-GCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
genomic: TTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|60396898|gb|DN229717.1|DN229717
EST:     GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
genomic: GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|33091899|gb|CF051893.1|CF051893
EST:     GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
genomic: GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|32937992|gb|CF042811.1|CF042811
EST:     GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
genomic: GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|211015403|gb|FL213617.1|FL213617
EST:     CATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
genomic: CATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|9953899|gb|BE640482.1|BE640482
EST:     GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
genomic: GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|13149409|gb|BG319731.1|BG319731
EST:     GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
genomic: GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
EST: gi|13557759|gb|BG549115.1|BG549115
EST:     GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAG                         AGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC
genomic: GGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTC

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: 311

GCTGCTGTCTATGGTGTGGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 337

GCTGCTGTCTATGGTGTGGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

GCTGCTGTCTATGGTGTGGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 300

GCTGCTGTCTATGGTGTGGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcag ... atgttttcagAGGCCTTATCAAAATTAAACAATGTTATAAGGCATCCTGATGCACGACTTCCTGATAATATCATGGCATATGACAATGCTGTTTCGGCGCTTGGAAAAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCTGTCTATGGTGTGGGTGTATGTGCCGAGTTTGGTGGTCATGTTTTTCGCCCTCTAGTAGGAGgtagattcagtacattttatatatgtgtttacacttatatttctcctgactttttccaacctatccaacaatgtgttgcttatgttttcag

- - - - - - - - - - - - - - - - -  TGGTGG