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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcgcatcttaacttttgacgcaatggtgttgtgtgtttatgatgtgcatgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAGGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTG

Basic information

species Zea mays
transcript GRMZM5G840582_T01
intron # 1
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|21390418|gb|BQ528467.1|BQ528467
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|21329817|gb|BQ485198.1|BQ485198
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|21329951|gb|BQ485332.1|BQ485332
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|32869764|gb|CF009446.1|CF009446
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|21391035|gb|BQ529084.1|BQ529084
EST:     GTCGTCCTACGGC-TGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|21329764|gb|BQ485131.1|BQ485131
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|87154658|gb|DY399447.1|DY399447
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|21329947|gb|BQ485328.1|BQ485328
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|71434127|gb|DR815177.1|DR815177
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|76011564|gb|DT938734.1|DT938734
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|76011565|gb|DT938735.1|DT938735
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|21480762|gb|BQ577445.1|BQ577445
EST:     GCGACGCATGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|21481419|gb|BQ578102.1|BQ578102
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|32870245|gb|CF009927.1|CF009927
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|50334092|gb|CO529218.1|CO529218
EST:     CTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: CTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|21481035|gb|BQ577718.1|BQ577718
EST:     CGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGA
genomic: CGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGG-CAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGA
EST: gi|21480829|gb|BQ577512.1|BQ577512
EST:     GTGACGCATGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|71431232|gb|DR812282.1|DR812282
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|21330134|gb|BQ485515.1|BQ485515
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|21626445|gb|BQ621366.1|BQ621366
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|32869036|gb|CF008718.1|CF008718
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|22545220|gb|BU097579.1|BU097579
EST:     GCGACGCANGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|87154082|gb|DY398871.1|DY398871
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|26455021|gb|CA826604.1|CA826604
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|32870282|gb|CF009964.1|CF009964
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|26455173|gb|CA826756.1|CA826756
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|21480818|gb|BQ577501.1|BQ577501
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|21480842|gb|BQ577525.1|BQ577525
EST:     GCGACGCANGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|50329733|gb|CO524859.1|CO524859
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|71431231|gb|DR812281.1|DR812281
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
EST: gi|21481144|gb|BQ577827.1|BQ577827
EST:     GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAG                         AAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG
genomic: GCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAG

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: 30 (upstream exon), 49 (downstream exon)
Score: 20

GGTAGGCCTCTTGAAAGTTCGTGTGGTCCGGGGTATCAACCTTGCCTACCGCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAGGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

GGTAGGCCTCTTGAAAGTTCGTGTGGTCCGGGGTATCAACCTTGCCTACCGCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAGGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTG


Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 7

GGTAGGCCTCTTGAAAGTTCGTGTGGTCCGGGGTATCAACCTTGCCTACCGCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAGGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTG


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 29

GGTAGGCCTCTTGAAAGTTCGTGTGGTCCGGGGTATCAACCTTGCCTACCGCGACGCAAGAGGCAGCGATCCGTATGTCGTCCTACGGCTTGGCAAGAAGgtgtgcgcat ... atgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAGGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatcttaacttttgacgcaatggtgttgtgtgtttatgatgtgcatgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAGGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTG
     ttaactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgcgcatcttaacttttgacgcaatggtgttgtgtgtttatgatgtgcatgcgtgcagAAACTGAAGACAAGCGTGAAGAAGAGATCCGTGAACCCCATATGGCAAGAGGAGCTAACTCTGACCGTCACAGATCCCAGCCAACCACTGAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG