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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgactggtccatatcagttggtttttagcttgaatctctctttttttttcattagttgatctctttcgtgtctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCCAGAGGAAATTTATGCGAAGCTTGTAGCTGCAAAGAATTTCCGTGCTGGC

Basic information

species Zea mays
transcript GRMZM2G133919_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 11
gtatgactggtccatatcagttggtttt--tagcttgaatctctctttttttttcattagttgatctctttcgtgtctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCCAGAGGAAATTTATGCGAAGCTTGTAGCTGCAAAGAATTTCCGTGCTGGC
||| ||  | ||  ||||| || |||||  || |||| | |  |     | |||  |||     |   |||   ||  ||  ||||||||||||||||||||||||||| ||||||||||| || |||  ||||||||||||||||||||| |||||||| ||||||||||||||||||||||||
gtaagatggatctgtatcattttgtttttttaacttgtagccttgaacctgttt-gttaaacagttgtttt---gttggtgccagGAATACTCTTTTGAGCATTGCAAAGCATTATGAAACAGGCGAACTTCTTCCAGAGGAAATTTATGCAAAGCTTGTCGCTGCAAAGAATTTCCGTGCTGGC
















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|20300828|gb|BQ163771.1|BQ163771
EST:     GATGCTGTAGAGTTCCCCTCCCAGTTCATGGAGA-CTGGTGCTATC-CAA                         GAAT-CTCTTTTGAGCATTGCAAAACATTATGAA-CCGGTG
genomic: GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTG
EST: gi|211206211|gb|FL245890.1|FL245890
EST:     GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAA                         GAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACCCTTCC
genomic: GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
EST: gi|6020894|gb|AW065822.1|AW065822
EST:     GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAA                         GAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACCCTTCC
genomic: GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
EST: gi|20507576|gb|BQ279691.1|BQ279691
EST:     GATGCTGTAGAGTTACCCTCCCAGCTCATGGAGAACTGGCGCTATCACAA                         GAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
genomic: GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
EST: gi|28909606|gb|CB331010.1|CB331010
EST:     GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGCGCTATCACAA                         GAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGCGAAACTCTTCC
genomic: GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
EST: gi|14242856|gb|BG840631.2|BG840631
EST:     AGAGTTACCCTCCCAGTT-ATGGAGAACTGGTGCTATCACAA                         GAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
genomic: AGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
EST: gi|67011759|gb|CO440508.1|CO440508
EST:     GATGCTGTACAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAA                         GAATACTCTTTTTGAGCATTTGCAAA-CATTATGAAAACGGGGAAACTCTT
genomic: GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTT-GAGCATT-GCAAAACATTATGAAACCGGTGAAACTCTT
EST: gi|31664241|gb|CD572966.1|CD572966
EST:     GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAA                         GAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGNGAAACTCTTCC
genomic: GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
EST: gi|67026706|gb|CO455455.1|CO455455
EST:     GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAA                         GAATACTCTTTTGAGCATTGCAAA-CATTATGAAACCGGTGAAACTCTTCC
genomic: GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
EST: gi|149009255|gb|EE153869.2|EE153869
EST:     GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAA                         GAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
genomic: GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
EST: gi|26456915|gb|CA828498.1|CA828498
EST:     GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAA                         GAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
genomic: GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
EST: gi|67025999|gb|CO454748.1|CO454748
EST:     GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAA                         GAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
genomic: GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCC
EST: gi|15554185|gb|BI644183.1|BI644183
EST:     GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAA                         GAATACTCTTTTGAGCATTGCA
genomic: GATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCA

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: 281

TTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCCAGAGGAAATTTATGCGAAGCTTGTAGCTGCAAAGAATTTCCGTGCTGGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 261

TTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCCAGAGGAAATTTATGCGAAGCTTGTAGCTGCAAAGAATTTCCGTGCTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

TTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCCAGAGGAAATTTATGCGAAGCTTGTAGCTGCAAAGAATTTCCGTGCTGGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 218

TTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgtatgactgg ... tctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCCAGAGGAAATTTATGCGAAGCTTGTAGCTGCAAAGAATTTCCGTGCTGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcttgaatctctctttttttttcattagttgatctctttcgtgtctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCCAGAGGAAATTTATGCGAAGCTTGTAGCTGCAAAGAATTTCCGTGCTGGC
                            agttgat  putative branch site (score: 218)
                                  tctctttcgtgtct  CT-rich tract
               tttttttttcattagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgactggtccatatcagttggtttttagcttgaatctctctttttttttcattagttgatctctttcgtgtctgtatcagGAATACTCTTTTGAGCATTGCAAAACATTATGAAACCGGTGAAACTCTTCCAGAGGAAATTTATGCGAAGCTTGTAGCTGCAAAGAATTTCCGTGCTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA