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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggattgtgttgaatttgtcaccctttgctttgatataagaacctctagttatatgctagaaggactaatcgttttggtgtgttgaaatggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGGCTGCTGCTGCCCCGGCTGTCGAGGAGAAGAAGGAAGAGGCCAAGGAGGA

Basic information

species Zea mays
transcript GRMZM2G032315_T01
intron # 3
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|14701090|gb|BI233508.1|BI233508
EST:     GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTG                         GTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCCCCTGCTGGTGGTGCTGCGG
genomic: GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGG
EST: gi|14701520|gb|BI233938.1|BI233938
EST:     GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTG                         GTGGCGGAGCTGCTCCA
genomic: GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCA
EST: gi|14701524|gb|BI233942.1|BI233942
EST:     GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTG                         GTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCCCCTGCTGGTGGTGCTGCGG
genomic: GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGG
EST: gi|14529509|gb|BI096642.1|BI096642
EST:     GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTG                         GTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCCCCTGCTGGTGGTGCTGCGG
genomic: GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGG
EST: gi|211349249|gb|FK973355.1|FK973355
EST:     GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTG                         GTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGG
genomic: GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGG
EST: gi|29543928|gb|CB604308.1|CB604308
EST:     GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTG                         GTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTG
genomic: GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTG
EST: gi|14529546|gb|BI096679.1|BI096679
EST:     GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTG                         GTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCCCCTGCTGGTGGTGCTGCGG
genomic: GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGG
EST: gi|15057120|gb|BI361092.1|BI361092
EST:     GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTG                         GTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCCCCTGCTGGTGGT
genomic: GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGT
EST: gi|211232580|gb|FK974101.1|FK974101
EST:     GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTG                         GTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTTCTGGTGGTGCTGCGG
genomic: GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGG
EST: gi|37394086|gb|CF634313.1|CF634313
EST:     GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTG                         GTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCCCCTGCTGGTGGTGCTGCGG
genomic: GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGG
EST: gi|113670812|gb|DW821054.1|DW821054
EST:     GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTG                         GTGGCGGAGACTGCTCCAGTTGCTGCTGCCG
genomic: GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAG-CTGCTCCAGTTGCTGCTGCCG
EST: gi|15177496|gb|BI398435.1|BI398435
EST:     GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTG                         GTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCCCCTGCTGGTGGTGCTGCGG
genomic: GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGG
EST: gi|211369682|gb|FK974192.1|FK974192
EST:     GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTG                         GTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGG
genomic: GCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGG

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: 49 (upstream exon), 49 (downstream exon)
Score: 726

AAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCCCTCTTCGCCAAGCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGGCTGCTGCTGCCCCGGCTGTCGAGGAGAAGAAGGAAGAGGCCAAGGAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 683

AAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCCCTCTTCGCCAAGCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGGCTGCTGCTGCCCCGGCTGTCGAGGAGAAGAAGGAAGAGGCCAAGGAGGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 597

AAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCCCTCTTCGCCAAGCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGGCTGCTGCTGCCCCGGCTGTCGAGGAGAAGAAGGAAGAGGCCAAGGAGGA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 242

AAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCCCTCTTCGCCAAGCTCCTGGAGAAGCGCAACGTCGAGGACCTCATCCTCTCCGTTGGATCTGgtatgcatcc ... ggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGGCTGCTGCTGCCCCGGCTGTCGAGGAGAAGAAGGAAGAGGCCAAGGAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctagttatatgctagaaggactaatcgttttggtgtgttgaaatggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGGCTGCTGCTGCCCCGGCTGTCGAGGAGAAGAAGGAAGAGGCCAAGGAGGA
                   gactaat  putative branch site (score: 242)
     ttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggattgtgttgaatttgtcaccctttgctttgatataagaacctctagttatatgctagaaggactaatcgttttggtgtgttgaaatggttttgtagGTGGCGGAGCTGCTCCAGTTGCTGCTGCCGCACCTGCTGGTGGTGCTGCGGCTGCTGCTGCCCCGGCTGTCGAGGAGAAGAAGGAAGAGGCCAAGGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - tgtgttg
- - - - - - - - - - - - -tttgctt
- - - - - - - - - - - - - - - - - - ataagaac