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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtattctggactctggagcactactaatattcattctagatcactgctttgtggtgagcttcaatgtcacgagtggttaattcattttgtaaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCATGGACAACAAAGAAAATACAG

Basic information

species Zea mays
transcript GRMZM2G058276_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 5
--tgtattctggactct-ggagcactactaatattcattctagatcactgctttgtggtgagcttcaatgtcacgagtggttaattcattttgtaaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCATGGACAACAAAGAAAATACAG
  || |||| |   | |    |||| |  || |   |   |          ||  ||  |  |   ||  || | | || |  |||  |||   ||| | ||||||||||||||||| | |||||||| ||||| ||||||||  | |  |||||||||||||||||||||| ||
gctgaattcagatttttcactgcaccaacaagaaaaaccatta--tgtgaattcatga-gtacactaacatctccaatgctccatttctttgtgaaactatagGTTACAGAATGGCTGTTGAGTGTGCTAGAAACGCTTTGCTGGAGAGGACCATGGACAACAAAGAAAATATAG
















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|211242377|gb|FL471585.1|FL471585
EST:     GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAG                         GTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGTTACAAAGGACCA
genomic: GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAGgtattacttg ... taaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCA
EST: gi|211486980|gb|FL134661.1|FL134661
EST:     GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAG                         GTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCA
genomic: GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAGgtattacttg ... taaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCA
EST: gi|211335042|gb|FL425887.1|FL425887
EST:     GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAG                         GTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCA
genomic: GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAGgtattacttg ... taaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCA
EST: gi|9952534|gb|BE639117.1|BE639117
EST:     GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAG                         GTTACAGAATGGCTCTCGA
genomic: GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAGgtattacttg ... taaattttagGTTACAGAATGGCTCTCGA
EST: gi|60400200|gb|DN233007.1|DN233007
EST:     GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAG                         GTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCA
genomic: GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAGgtattacttg ... taaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCA
EST: gi|32909064|gb|CF013876.1|CF013876
EST:     GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAG                         GTTACAGAATGGCTCTCGAGTGTGCCAGAAATGGCTTTGCTACAAAATACC
genomic: GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAGgtattacttg ... taaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATG-CTTTGCTACAAAATACC
EST: gi|211346060|gb|FL392059.1|FL392059
EST:     GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAG                         GTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCA
genomic: GGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAGgtattacttg ... taaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCA

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: 531

GGTGATGGGACAACTTCTGTTGTTGTTCTAGCTGGAGAACTTTTGAAGGAGGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAGgtattacttg ... taaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCATGGACAACAAAGAAAATACAG


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

GGTGATGGGACAACTTCTGTTGTTGTTCTAGCTGGAGAACTTTTGAAGGAGGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAGgtattacttg ... taaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCATGGACAACAAAGAAAATACAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 222

GGTGATGGGACAACTTCTGTTGTTGTTCTAGCTGGAGAACTTTTGAAGGAGGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAGgtattacttg ... taaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCATGGACAACAAAGAAAATACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

GGTGATGGGACAACTTCTGTTGTTGTTCTAGCTGGAGAACTTTTGAAGGAGGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAGgtattacttg ... taaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCATGGACAACAAAGAAAATACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctttgtggtgagcttcaatgtcacgagtggttaattcattttgtaaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCATGGACAACAAAGAAAATACAG
                              ggttaat  putative branch site (score: 248)
                                ttaattcattttgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtattctggactctggagcactactaatattcattctagatcactgctttgtggtgagcttcaatgtcacgagtggttaattcattttgtaaattttagGTTACAGAATGGCTCTCGAGTGTGCCAGAAATGCTTTGCTACAAAATACCATGGACAACAAAGAAAATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - -ctggagc
- - - - - - - - - - - - - - - - - - - - - - ctgcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcttca