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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgttgtatttgggcttgagcatggtactggttgtacaaccagaaggtttcattgtcatttctgtatattgagctaatagctttcacttacacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCCGTTACAACCCTCTCCGATGTTGAGGGGCTATGTGTTTCTTTTGCTGGGA

Basic information

species Zea mays
transcript GRMZM2G458549_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458549_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g61710.1 (Oryza sativa), 3'ss of exon 7
ctgttgtatttgggcttgagcatggtactggttgtacaaccagaaggtttcattgtcatttctgtatattgagctaatagctttcacttacactttt-cagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCCGTTACAACCCTCTCCGATGTTGAGGGGCTATGTGTTTCTTTTGCTGGGA
   ||| |  |||  ||||||  | | ||   |   |||| |     |   ||| || |||   | | || |  |||||    |   || || |||| ||||||||||||||||||||||| |||||||| |  ||||||||| ||||||| ||||| |||||||| |||||||||||| ||||||| ||||||||||| |
actttggaactggatttgagctggctgctatatcaccaacaaagtaatgatatt-tctttttcatttgttcatttaatattgctgttttgcatttttgcagATTGTTCTTGCCATCAAACTAGGGATGGAAACAAAAAAGGCTGTCTCCTCTGTTACCACCCTCTCTGATGTTGAGGGGTTATGTGTCTCTTTTGCTGGAA
















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|50330093|gb|CO525219.1|CO525219
EST:     CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCACCG                         ATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCT
genomic: CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCT
EST: gi|78111011|gb|DV529408.1|DV529408
EST:     CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCG                         ATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
genomic: CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
EST: gi|32833835|gb|CD973513.1|CD973513
EST:     CAGCTGCAACAAATTATAATACCCGTGTTGTGGAGTGTCGCTTAGCAGCG                         ATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
genomic: CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
EST: gi|17921536|gb|BM259187.1|BM259187
EST:     CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCG                         ATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
genomic: CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
EST: gi|211541591|gb|FL022794.1|FL022794
EST:     AATAACCGCGTTGTGGAGTGTCGCTTAGCAGCG                         ATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAAGCTATCTCCTCC
genomic: AATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
EST: gi|17921866|gb|BM259517.1|BM259517
EST:     CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCG                         ATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
genomic: CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
EST: gi|32943061|gb|CF047880.1|CF047880
EST:     CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCG                         ATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
genomic: CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
EST: gi|211541592|gb|FL022795.1|FL022795
EST:     TAATAACCGCGTTGTGGAGTGTCGCTTAGCAGCG                         ATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAAGCTATCTCCTCC
genomic: TAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
EST: gi|32835728|gb|CD975406.1|CD975406
EST:     CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCG                         ATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
genomic: CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC
EST: gi|211139371|gb|FL028742.1|FL028742
EST:     CAGCTGCAACAANTTATAATAACCGCGTTGTGGAGTGTCGCTTANCAGCG                         ATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAAGCTATCTCCTCC
genomic: CAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCC

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: 45 (upstream exon), 49 (downstream exon)
Score: 54

TGGTACATTTGTGATCGCCCATTGTTTGGCCGAGTCCAAGAAAGCAGAGACAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCCGTTACAACCCTCTCCGATGTTGAGGGGCTATGTGTTTCTTTTGCTGGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 111

TGGTACATTTGTGATCGCCCATTGTTTGGCCGAGTCCAAGAAAGCAGAGACAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCCGTTACAACCCTCTCCGATGTTGAGGGGCTATGTGTTTCTTTTGCTGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

TGGTACATTTGTGATCGCCCATTGTTTGGCCGAGTCCAAGAAAGCAGAGACAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCCGTTACAACCCTCTCCGATGTTGAGGGGCTATGTGTTTCTTTTGCTGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

TGGTACATTTGTGATCGCCCATTGTTTGGCCGAGTCCAAGAAAGCAGAGACAGCTGCAACAAATTATAATAACCGTGTTGTGGAGTGTCGCTTAGCAGCGgtaaatgact ... cacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCCGTTACAACCCTCTCCGATGTTGAGGGGCTATGTGTTTCTTTTGCTGGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttcattgtcatttctgtatattgagctaatagctttcacttacacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCCGTTACAACCCTCTCCGATGTTGAGGGGCTATGTGTTTCTTTTGCTGGGA
                                       cacttac  putative branch site (score: 157)
                                             cacttttc  CT-rich tract
                 tgtatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgttgtatttgggcttgagcatggtactggttgtacaaccagaaggtttcattgtcatttctgtatattgagctaatagctttcacttacacttttcagATTGTTCTTGCCATCAAACTTGGGATGGATAGGAAAAAGGCTATCTCCTCCGTTACAACCCTCTCCGATGTTGAGGGGCTATGTGTTTCTTTTGCTGGGA

ctgttgt
- - - - - -gggcttg
- - - - - - - - - - - -ggtactg
- - - - - - - - - - - - - - - - - -acaacca
- - - - - - - - - - - - - - - - - - - - - - - -tttcatt