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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacacttatttcacaggagatgggttccatttttgtacaccacgaacaagaaatcactttgtttagactgccaaacatatactgtacttgagcctttgtgactgcttttccttgatctgctgttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTGAGATGGGCGGAAGAGAAAGAACATGCTGATGAGTCTGATAAAGTTTTTG

Basic information

species Zea mays
transcript GRMZM5G806257_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G806257_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g56740.2 (Oryza sativa), 3'ss of exon 12
----gtaacac-ttatttcacaggagatgggttccatttttgtacaccacgaacaagaaatcactttgtttagactgccaa-acatatactgtac-ttga--gcctttgtgactgcttttc---cttgatc---tgctgttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTGAGATGGGCGGAAGAGAAAGAACATGCTGATGAGTCTGATAAAGTTTTTG
      |||   | |||  ||    | |  |||   ||||| |       |     | |     | | |      |||    |||     ||| | ||||  | | |||||| |   |||     |||||     ||| |||||| ||||||||||| ||||||||||||| |||||||||||||||||| |||||||||||||||||||| ||||||||| |||| ||||| |||||||| ||||| |
gtaaacaacttatcattgtactcttgttttgttgtgttttttttttgggtgtgtgtggagcacatatatcctatttgcttgcacactccttgtccattgaatgtccttgtgattctcttttggttttgataatacgctattgaacacagATCTTGCCTTACCTCTATGATAAGGAGGTAGTAAGTGAAGACGCAATTTTGAGATGGGCGGAGGAGAAAGAAAATGCCGATGAATCTGATAAGGTTTTCG
















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|60356359|gb|DN223332.1|DN223332
EST:     AGGAAATGTGTCAAGAGACCACAAAAGANNNNNNNCCGCTGTTTCCAAAG                         ATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
genomic: AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
EST: gi|91867732|gb|EB399773.1|EB399773
EST:     AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAG                         ATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
genomic: AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
EST: gi|5525495|gb|AI861388.1|AI861388
EST:     AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAG                         ATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
genomic: AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
EST: gi|67025171|gb|CO453920.1|CO453920
EST:     AGGAAATGTGTCAAGAGAC-ACAAAAGATTTTCCTC-GCTGTTTCCAA-G                         ATCTTGC-ATACCTCTATGATACGGAG-TAGTAA
genomic: AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAA
EST: gi|8102881|gb|AW927559.1|AW927559
EST:     AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAG                         ATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
genomic: AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
EST: gi|8102880|gb|AW927558.1|AW927558
EST:     AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAG                         ATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
genomic: AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
EST: gi|5325105|gb|AI783296.1|AI783296
EST:     AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAG                         ATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
genomic: AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
EST: gi|32933173|gb|CF037985.1|CF037985
EST:     AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAG                         ATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
genomic: AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
EST: gi|118406765|gb|EH038213.1|EH038213
EST:     AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAG                         ATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
genomic: AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
EST: gi|5804618|gb|AI979588.1|AI979588
EST:     AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAG                         ATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
genomic: AGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
EST: gi|5714177|gb|AI944162.1|AI944162
EST:     CCGCTGTTTCCAAAG                         ATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG
genomic: CCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTG

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: 46 (upstream exon), 49 (downstream exon)
Score: 75

ATGGAGATACTTTTAAAGTTTGAGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTGAGATGGGCGGAAGAGAAAGAACATGCTGATGAGTCTGATAAAGTTTTTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 64

ATGGAGATACTTTTAAAGTTTGAGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTGAGATGGGCGGAAGAGAAAGAACATGCTGATGAGTCTGATAAAGTTTTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

ATGGAGATACTTTTAAAGTTTGAGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTGAGATGGGCGGAAGAGAAAGAACATGCTGATGAGTCTGATAAAGTTTTTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 48

ATGGAGATACTTTTAAAGTTTGAGGAAATGTGTCAAGAGACCACAAAAGATTTTTCTCCGCTGTTTCCAAAGgtaacactta ... ttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTGAGATGGGCGGAAGAGAAAGAACATGCTGATGAGTCTGATAAAGTTTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatactgtacttgagcctttgtgactgcttttccttgatctgctgttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTGAGATGGGCGGAAGAGAAAGAACATGCTGATGAGTCTGATAAAGTTTTTG
                                ccttgat  putative branch site (score: 48)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacacttatttcacaggagatgggttccatttttgtacaccacgaacaagaaatcactttgtttagactgccaaacatatactgtacttgagcctttgtgactgcttttccttgatctgctgttgaacgcagATCTTGCCATACCTCTATGATACGGAGGTAGTAAGTGAAGATGCAATTTTGAGATGGGCGGAAGAGAAAGAACATGCTGATGAGTCTGATAAAGTTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT