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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtactcagtgtcgatctgctaagattagtagtgaatggaatgacagatagccgccgggacggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGAGTTCACCAGCAGATTCACGTGGACCGGCTCAATGGCATGATCGGTGGCA

Basic information

species Zea mays
transcript GRMZM2G042080_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042080_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g02500.1 (Oryza sativa), 3'ss of exon 2
gtatgtactcag-tgtcgatctgctaagattagtagtgaatgg-aatgacagatagccgccgggacggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGAGTTCACCAGCAGATTCACGTGGACCGGCTCAATGGCATGATCGGTGGCA
||| |||| ||  |  | || ||    | || | |  || | | | |||||  |    |  ||||    |||||||||||| || ||||||||||| ||||||||||||||||| ||||||||||||||||| ||| | |||||||| ||  |||||||||||||||| |||||||
gtaagtacacaaataccaatttgt--ggttttgcacagagtagtagtgacaactgtgtgatggga----aatgtagGATGCCCTAGAGCCATACATCAGCAAGGAGACGGTGGAACAGCACTGGGGAGTTCATCAGAACATTCACGTCGAGAGGCTCAATGGCATGATTGGTGGCA
















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|76932372|gb|DV173030.1|DV173030
EST:     TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
EST: gi|211287064|gb|FL337506.1|FL337506
EST:     TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGC
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGC
EST: gi|76287059|gb|DV026627.1|DV026627
EST:     TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
EST: gi|211260647|gb|FL352281.1|FL352281
EST:     TGCCTGAGGACGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAA
EST: gi|71421895|gb|DR805584.1|DR805584
EST:     TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
EST: gi|148959395|gb|EC905430.2|EC905430
EST:     TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
EST: gi|89252849|gb|DY624635.1|DY624635
EST:     TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
EST: gi|33467070|gb|CF244119.1|CF244119
EST:     TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
EST: gi|148935525|gb|EC879566.2|EC879566
EST:     TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
EST: gi|149075255|gb|EE163758.2|EE163758
EST:     TGCCTGAGGACGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
EST: gi|148993468|gb|EE033787.2|EE033787
EST:     TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
EST: gi|50329231|gb|CO524357.1|CO524357
EST:     TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
EST: gi|211241657|gb|FL328636.1|FL328636
EST:     TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGA
EST: gi|5398723|gb|AI812188.1|AI812188
EST:     TGCCTGAGGACGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
EST: gi|211290848|gb|FL314519.1|FL314519
EST:     TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAKACGGTGGAGCAGCACTGGGGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
EST: gi|50331822|gb|CO526948.1|CO526948
EST:     TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTG                         GATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA
genomic: TGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGA

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: 38 (upstream exon), 49 (downstream exon)
Score: 62

TGACGCCATTGATGCTGATGTTGGTACCGAAGATGAACTGGAGTCTTCGCTGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGAGTTCACCAGCAGATTCACGTGGACCGGCTCAATGGCATGATCGGTGGCA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 56

TGACGCCATTGATGCTGATGTTGGTACCGAAGATGAACTGGAGTCTTCGCTGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGAGTTCACCAGCAGATTCACGTGGACCGGCTCAATGGCATGATCGGTGGCA


Block sizes: 20 (upstream exon), 49 (downstream exon)
Score: 9

TGACGCCATTGATGCTGATGTTGGTACCGAAGATGAACTGGAGTCTTCGCTGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGAGTTCACCAGCAGATTCACGTGGACCGGCTCAATGGCATGATCGGTGGCA


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 9

TGACGCCATTGATGCTGATGTTGGTACCGAAGATGAACTGGAGTCTTCGCTGCCTGAGGATGTTGAGTGGATAAAGCAGCAGCCACTTCCTTATCCTTTGgtatgtactc ... ggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGAGTTCACCAGCAGATTCACGTGGACCGGCTCAATGGCATGATCGGTGGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctaagattagtagtgaatggaatgacagatagccgccgggacggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGAGTTCACCAGCAGATTCACGTGGACCGGCTCAATGGCATGATCGGTGGCA
     aagatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtactcagtgtcgatctgctaagattagtagtgaatggaatgacagatagccgccgggacggtaatgtagGATGCTCTGGAGCCATACATAAGCAAGGAGACGGTGGAGCAGCACTGGGGAGTTCACCAGCAGATTCACGTGGACCGGCTCAATGGCATGATCGGTGGCA

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