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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttatttaaaattttaaaaaaaatccaatgtgatgaccgtgtagacatgttcataatttggaaatgttgtgaaatccccgcag

Basic information

species Zea mays
transcript GRMZM2G133988_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133988_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 5'ss of exon 13
GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttt------tatttaaaattttaaa-----aaaaatccaatgtgatgaccgtgtagacatgtt-cataatttggaaatgttgtgaaatccccgcag------------------------
||||||||||| |||||||||||||| ||||||||||| || ||||||||||      | | |   | | |||      | | ||    || || ||   |  | |  | |      |  | ||    |  | ||        ||                        
GGAAAGAAGGTCAAAGTTCCCACATTCCTTGTCCCTGCAACCCAAAAGgtttgtataatttgttgcactgtaagtgttgatagatttgttgggaagattctagaaatttatcatgggaactagattaatcataaatggattatagtaattcatatattaaaatcttcag

upper sequence: GRMZM2G133988_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 13
GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttatttaaaattttaa--aaaaaatccaatgtgatgaccgtgtagacatgttcataatttggaaatgttgtgaaatccccgcag-----------------------------
||||||||||| |||||||||||||||||||||||||| || ||||||||||    |  | ||||     |   ||       || ||      | |    ||  | ||  | ||  |||   ||  |  ||||                              
GGAAAGAAGGTCAAAGTTCCCACATTTCTTGTCCCTGCAACCCAAAAGgtttgtactgtatttttgcttgatggatttgtatggaagattccaaatagggatttgtcataggaaagagtt--taatcctacgcaatatagtaattgatatgataaaattatcag
















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|211485260|gb|FL406758.1|FL406758
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGNCCCTGCCACGCAAAAG                         GTGTGGTTGNACGTATATAGCCTCCCTGTACCAGGATCTGGNGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
EST: gi|13382157|gb|BG458832.1|BG458832
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG                         GTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
EST: gi|211084567|gb|FL380768.1|FL380768
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAG                         GTGTGGTTGTACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
EST: gi|211445219|gb|FL371640.1|FL371640
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAG                         GTGTGGTTGTACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
EST: gi|211476197|gb|FL374877.1|FL374877
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAG                         GTGTGGTTGTACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
EST: gi|37381215|gb|CF627478.1|CF627478
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG                         GTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
EST: gi|211199607|gb|FL408270.1|FL408270
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAG                         GTGTGGTTGTACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
EST: gi|211413964|gb|FL425524.1|FL425524
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAG                         GTGTGGTTGTACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
EST: gi|211201683|gb|FL384209.1|FL384209
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAG                         GTGTGGTTGTACCGTAATATAGCCTCCCTG
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGAC-GTA-TATAGCCTCCCTG
EST: gi|32849674|gb|CD989355.1|CD989355
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG                         GTGTGGTTGGACATATATAGCCTTCCTGTA
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTA
EST: gi|31356659|gb|CD441016.1|CD441016
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG                         GTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
EST: gi|211181797|gb|FL472359.1|FL472359
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAG                         GTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
EST: gi|33100114|gb|CF060074.1|CF060074
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG                         GTGTGGTTGGACATATATAGCCTCCCTGT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGT
EST: gi|211282426|gb|FL393385.1|FL393385
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAG                         GTGTGGTTGTACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
EST: gi|211228096|gb|FL409262.1|FL409262
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAG                         GTGTGGTTGTACGTATATANCCTCCCTGTACCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT

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: 47 (upstream exon), 41 (downstream exon)
Score: 33

GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACTTGCTCCCAGGTATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 104

GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACTTGCTCCCAGGTATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 51

GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACTTGCTCCCAGGTATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTA


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 43

GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttattta ... atccccgcagGTGTGGTTGGACGTATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACTTGCTCCCAGGTATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACGCAAAAGgttttatttaaaattttaaaaaaaatccaatgtgatgaccgtgtagacatgttcataatttggaaatgttgtgaaatccccgcag

- AAAGAA
-  AAGAAG