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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagcttctttcacattatttcaataagacctgtggggtccttatgtttcagctctgaaagataatctatgcatactcag

Basic information

species Zea mays
transcript GRMZM2G023652_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023652_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os11g36340.1 (Oryza sativa), 5'ss of exon 7
TTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagcttctttcacattatttcaataagacctgtggg-gtccttatgtttcagctctgaaagataatctatgcatactcag
|| | |||||| ||||||||||| ||||| ||||||||||| ||| |||||||| ||||||  |||||||| |||||| | | ||| | || |||   |||| || | ||    |   ||    |  | |||||||  ||||||||   |||||||
TTCTACCAAAAACTTGAAGAGAAGATCCATGCAAAGGAGCTTGAACAAACAAATTTGCAGGCAAAATCTAAAgtgagaacctttttgatatcattaatataaaacttttgaatatttgtaccacttggatctgaaaattaatctat---tactcag
















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|32838814|gb|CD978495.1|CD978495
EST:     AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG                         GAGAGCCAAGAGGCTGAGATCAAACTGCTCAGGAAGAGCCTAACATTTAAA
genomic: AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
EST: gi|22819173|gb|BU499263.1|BU499263
EST:     AAACAAATCTGCAGGAGAAATCTAAG                         GAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTT-AA
genomic: AAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
EST: gi|21843366|gb|BQ703947.1|BQ703947
EST:     AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG                         GAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
genomic: AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
EST: gi|32833164|gb|CD972842.1|CD972842
EST:     AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG                         GAGAGCCAAGAGGCTGAGATCAAACTGCTCAGGAAGAGCCTAACATTTAAA
genomic: AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
EST: gi|87157517|gb|DY402306.1|DY402306
EST:     AATCTGCAGGAGAAATCTAAG                         GAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
genomic: AATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
EST: gi|21809702|gb|BQ668020.1|BQ668020
EST:     AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG                         GAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
genomic: AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
EST: gi|32839274|gb|CD978955.1|CD978955
EST:     AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG                         GAGAGCCAAGAGGCTGAGATCAAACTGCTCAGGAAGAGCCTAACATTTAAA
genomic: AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
EST: gi|31355396|gb|CD439753.1|CD439753
EST:     AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG                         GAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
genomic: AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
EST: gi|32837723|gb|CD977401.1|CD977401
EST:     AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG                         GAGAGCCAAGAGGCTGAGATCAAACTGCTCAGGAAGAGCCTAACATTTAAA
genomic: AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
EST: gi|22542624|gb|BU093062.1|BU093062
EST:     AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG                         GAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTAAAA
genomic: AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
EST: gi|31355088|gb|CD439445.1|CD439445
EST:     AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAG                         GAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA
genomic: AAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 377

TTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAAGCCACACCTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

TTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAAGCCACACCTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 348

TTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAAGCCACACCTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 312

TTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagctt ... gcatactcagGAGAGCCAAGAGGCTGAGATCAAACTGCTGAGGAAGAGCCTAACATTTAAAGCCACACCTATGCCAAGCTTTTACAAGGAGCAGCCACCCAAAGTTGAGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTTCCAAAAGCTTGAAGAGAAAATCCACGCAAAGGAGCTGGAAAAAACAAATCTGCAGGAGAAATCTAAGgtgagagcttctttcacattatttcaataagacctgtggggtccttatgtttcagctctgaaagataatctatgcatactcag

- - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA