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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaatatctagttttaaattcattttagcttgtgttattagtatgcttcatttataagtatatttgataacattgtctgctgtatgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTGCCCGGATCCCAGAATCGTAACAGTTTGCTTGGAGGGTCTCGAGAACATC

Basic information

species Zea mays
transcript GRMZM2G088088_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088088_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g06350.1 (Oryza sativa), 3'ss of exon 9
gtatgcaaatatctagt-tttaaattcattttagcttgtgttattagtatgcttcatttataagtata-tttgataacattgtctgctgtatgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTGCCCGGATCCCAGAATCGTAACAGTTTGCTTGGAGGGTCTCGAGAACATC
||||||   | | |  | |||  |||  || |   |  | ||  ||| ||  ||||||  | | |||  |||| | |||   | ||   | |  |    |||||||||||||||||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||||||||| ||||| |||||||||
gtatgccttttttttttctttgcattacttgtgtataatatttatagaatttttcatt-gtcattatggtttgctcacaacatatgaaatgtcgacc--agGTACCTTGTTGCCCAGGGTTGCATCAAGCCACTCTGTGATCTGCTTGTTTGCCCAGATCCCAGGATCGTGACAGTTTGCTTGGAAGGTCTTGAGAACATC
















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|6564217|gb|AW231839.1|AW231839
EST:     GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAA                         GTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
genomic: GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAAgtatgcaaat ... tgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
EST: gi|213179381|gb|FM182985.1|FM182985
EST:     GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAA                         GTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
genomic: GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAAgtatgcaaat ... tgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
EST: gi|60338095|gb|DN205068.1|DN205068
EST:     GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAA                         GTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
genomic: GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAAgtatgcaaat ... tgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
EST: gi|30705724|gb|CD058895.1|CD058895
EST:     GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAA                         GTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
genomic: GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAAgtatgcaaat ... tgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
EST: gi|6587581|gb|AW244899.1|AW244899
EST:     GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAA                         GTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
genomic: GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAAgtatgcaaat ... tgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
EST: gi|211452349|gb|FL292614.1|FL292614
EST:     GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAA                         GTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
genomic: GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAAgtatgcaaat ... tgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
EST: gi|40337118|gb|CK371188.1|CK371188
EST:     CCTGCGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAA                         GTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
genomic: CCTG-GGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAAgtatgcaaat ... tgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
EST: gi|211452353|gb|FL292618.1|FL292618
EST:     GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAA                         GTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG
genomic: GCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAAgtatgcaaat ... tgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTG

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), 47 (downstream exon)
Score: 408

CTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAAgtatgcaaat ... tgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTGCCCGGATCCCAGAATCGTAACAGTTTGCTTGGAGGGTCTCGAGAACATC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 391

CTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAAgtatgcaaat ... tgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTGCCCGGATCCCAGAATCGTAACAGTTTGCTTGGAGGGTCTCGAGAACATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 319

CTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAAgtatgcaaat ... tgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTGCCCGGATCCCAGAATCGTAACAGTTTGCTTGGAGGGTCTCGAGAACATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 410

CTCTGGTGCAACTCCTGCAAACTGCTGAATTTGACATCAAGAAAGAAGCAGCCTGGGCAATTTCAAATGCCACTTCTGGTGGCACACATGATCAGATCAAgtatgcaaat ... tgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTGCCCGGATCCCAGAATCGTAACAGTTTGCTTGGAGGGTCTCGAGAACATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatgcttcatttataagtatatttgataacattgtctgctgtatgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTGCCCGGATCCCAGAATCGTAACAGTTTGCTTGGAGGGTCTCGAGAACATC
                         tgataac  putative branch site (score: 410)
       ttcatttataagtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaaatatctagttttaaattcattttagcttgtgttattagtatgcttcatttataagtatatttgataacattgtctgctgtatgaaatgtagGTACCTTGTTGCCCAGGGTTGCATTAAGCCACTCTGTGATCTGCTTGTTTGCCCGGATCCCAGAATCGTAACAGTTTGCTTGGAGGGTCTCGAGAACATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG