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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcgtcgcgctctctctcacacacgcacgcacacaaagttgtcttcgtgtctgaatcctgcactacttccgtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTGCTATCCTGCATGGATGTCTTAGCCAGTGCTTCATTCCATTGCCTTGAGA

Basic information

species Zea mays
transcript GRMZM2G087095_T01
intron # 7
splice site 3'
intron type U2

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|211463197|gb|FL126646.1|FL126646
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|32808460|gb|CD960694.1|CD960694
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|211318376|gb|FL452472.1|FL452472
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|78122333|gb|DV540717.1|DV540717
EST:     CCAGAACACTTTTTCCAGGTTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|50331175|gb|CO526301.1|CO526301
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|32838769|gb|CD978450.1|CD978450
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGC
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGC
EST: gi|18383542|gb|BM416742.1|BM416742
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|211167531|gb|FL479829.1|FL479829
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|78112770|gb|DV531164.1|DV531164
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|76285512|gb|DV025080.1|DV025080
EST:     CAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGNCA-CCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCT
genomic: CAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTG-CAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCT
EST: gi|21809510|gb|BQ667828.1|BQ667828
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|71425166|gb|DR806565.1|DR806565
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|148951816|gb|EC897579.2|EC897579
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|26557907|gb|CA830142.1|CA830142
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|211064908|gb|FL126262.1|FL126262
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|71421466|gb|DR805441.1|DR805441
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|5055580|gb|AI734467.1|AI734467
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|32847296|gb|CD986977.1|CD986977
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|71421467|gb|DR805442.1|DR805442
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|76285511|gb|DV025079.1|DV025079
EST:     CCAGAACACTTTTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|5030602|gb|AI714796.1|AI714796
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|21809509|gb|BQ667827.1|BQ667827
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|32835484|gb|CD975162.1|CD975162
EST:     CAGAACACTTCTTCCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGC
genomic: CAGAACACTTCTTCC-AGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGC
EST: gi|71330054|gb|DR801766.1|DR801766
EST:     CCAGAACACTTTTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|87157198|gb|DY401987.1|DY401987
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
EST: gi|71425163|gb|DR806564.1|DR806564
EST:     CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTAC                         ATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG
genomic: CCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 228

AGTTAGCGTGGCAAGGCGAAGGCGGCATGTTGTCCCATGACCCTCCACAGCCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTGCTATCCTGCATGGATGTCTTAGCCAGTGCTTCATTCCATTGCCTTGAGA


Block sizes: 24 (upstream exon), 26 (downstream exon)
Score: 2

AGTTAGCGTGGCAAGGCGAAGGCGGCATGTTGTCCCATGACCCTCCACAGCCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTGCTATCCTGCATGGATGTCTTAGCCAGTGCTTCATTCCATTGCCTTGAGA


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 81

AGTTAGCGTGGCAAGGCGAAGGCGGCATGTTGTCCCATGACCCTCCACAGCCAGAACACTTCTTCCAGGCTCTGGAGAGCAACCCATGTCTGCAACCTACgtaattcgtc ... gtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTGCTATCCTGCATGGATGTCTTAGCCAGTGCTTCATTCCATTGCCTTGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacgcacacaaagttgtcttcgtgtctgaatcctgcactacttccgtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTGCTATCCTGCATGGATGTCTTAGCCAGTGCTTCATTCCATTGCCTTGAGA
                                        cttccgttt  CT-rich tract
                                              tttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcgtcgcgctctctctcacacacgcacgcacacaaagttgtcttcgtgtctgaatcctgcactacttccgtttatgcagATACCATACGATGGACATGAACCAGCAGCCAGTGCCAGCGCCGGGCGGCTGCTATCCTGCATGGATGTCTTAGCCAGTGCTTCATTCCATTGCCTTGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA