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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcttaacatgataaaatctaaagatttatatctttagatattttttggacgatttttgcttagataagagcataagtactgtttgaactacttaatgatatcactgaaccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG

Basic information

species Zea mays
transcript GRMZM2G097059_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097059_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g32948.1 (Oryza sativa), 3'ss of exon 5
gtatgctcttaacatgataaaatctaaagatttatatctttagatattttttggacgatttttgcttagataagagcata-agtactgtttgaactacttaatgatatcactgaaccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
                            |    |  |    | | |  ||    || || | |  | ||  ||||  ||  | || |     |||||  |  | ||||  || || ||| | ||||| |||||| |||||||||||||||||||||| |||||||| 
----------------------------gtacaagcttgacataaaacttaccaactatgtat-ttcaggcaagaaaatttattatttccaaaactaact--ttatatacctaaatcattttcagGAACAAATGTTGTGTGAAGCAAATAAGTGCCTCAGAAGAAAA
















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|32833483|gb|CD973161.1|CD973161
EST:     ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGG                         GAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
genomic: ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGGgtatgctctt ... ccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
EST: gi|67039080|gb|CO465335.1|CO465335
EST:     ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGG                         GAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
genomic: ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGGgtatgctctt ... ccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
EST: gi|78115260|gb|DV533648.1|DV533648
EST:     ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGG                         GAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
genomic: ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGGgtatgctctt ... ccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
EST: gi|32839046|gb|CD978727.1|CD978727
EST:     ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGG                         GAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
genomic: ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGGgtatgctctt ... ccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
EST: gi|78074567|gb|DV503001.1|DV503001
EST:     ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGG                         GAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
genomic: ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGGgtatgctctt ... ccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
EST: gi|8665529|gb|BE186345.1|BE186345
EST:     ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGG                         GAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
genomic: ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGGgtatgctctt ... ccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
EST: gi|67016010|gb|CO444759.1|CO444759
EST:     ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGG                         GAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
genomic: ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGGgtatgctctt ... ccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
EST: gi|87153067|gb|DY397856.1|DY397856
EST:     ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGG                         GAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
genomic: ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGGgtatgctctt ... ccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
EST: gi|8383276|gb|BE056219.1|BE056219
EST:     ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGG                         GAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
genomic: ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGGgtatgctctt ... ccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
EST: gi|18648993|gb|BM497812.1|BM497812
EST:     ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGG                         GAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
genomic: ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGGgtatgctctt ... ccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG

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), 49 (downstream exon)
Score: 206

ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGGgtatgctctt ... ccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG


Block sizes: 24 (upstream exon), 26 (downstream exon)
Score: 1

ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGGgtatgctctt ... ccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 441

ACACAGCATATGCTTGATCAGCTCACTGATCTTCAGAGGAGGgtatgctctt ... ccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagagcataagtactgtttgaactacttaatgatatcactgaaccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG
                          acttaat  putative branch site (score: 441)
                            ttaatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctcttaacatgataaaatctaaagatttatatctttagatattttttggacgatttttgcttagataagagcataagtactgtttgaactacttaatgatatcactgaaccatgtccagGAGCAAATGATGTGTGAAGCAAATAAGTGCCTTAGAAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA