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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattactgttcttggcttctctccagctaattatgatacagtaacgttttatggcattgatcactgatatctggtgaagtgtag

Basic information

species Zea mays
transcript GRMZM2G009876_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 5'ss of exon 4
---GCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtga--attactgttcttggct------------tctctccag---ctaattatgatacag----taacgttttatggcattgatcactgatatctggtgaagtgtag
   ||||||||| |||| |   || ||||||||||||||||   | |||||||||||||||||||| ||||||||||| |||||||||||||| || || ||||| |  | |  | || | || |            ||| || |    |||  | |||||||      ||| ||| |  |  ||||||| | ||||   |||||   |||
AATGCACGACGAGTCAACTTCTCGGCAGAAGGTTGATGATG---TTCAAGAGGGTGCTCTTCCTCCATATCTGCTGGACCGTGATCAGACACAACGTGCCAAGgtaagtactcatattttgggttgctaaaatgctatctttctataatctagatgtgatacacaagtcaacttttcactgttttgatcattcatatgctgtgaaacatag
















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|211143002|gb|FL390386.1|FL390386
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211452151|gb|FL396750.1|FL396750
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAA
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAA
EST: gi|101382315|gb|EB813213.1|EB813213
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|74232800|gb|DT640714.1|DT640714
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211129107|gb|FL371425.1|FL371425
EST:     GTGCTCTTCCTCCGTATCTGTTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211527014|gb|FL385877.1|FL385877
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGACCAGACACAGCGCGCTAAG                         GTCCTCAGCAACACAAT
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAAT
EST: gi|101390908|gb|EB817389.1|EB817389
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|6918424|gb|AW399954.1|AW399954
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|74232799|gb|DT640713.1|DT640713
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|67038385|gb|CO464715.1|CO464715
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|101392350|gb|EB818104.1|EB818104
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211049010|gb|FL423464.1|FL423464
EST:     GTGCTCTTCCTCCGTATCTGTTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211358243|gb|FL402304.1|FL402304
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|148953095|gb|EE152575.2|EE152575
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|31350057|gb|CD434414.1|CD434414
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|29946118|gb|CB815988.1|CB815988
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211133673|gb|FL369483.1|FL369483
EST:     GTGCTCTTCCTCCGTATCTGTTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|60399997|gb|DN232804.1|DN232804
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|76015209|gb|DT942379.1|DT942379
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|60351247|gb|DN218220.1|DN218220
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|88757436|gb|DY541577.1|DY541577
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211113966|gb|FL427446.1|FL427446
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|149027253|gb|EE046450.2|EE046450
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
EST: gi|211300841|gb|FL383944.1|FL383944
EST:     GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAG                         GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG
genomic: GTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 204

GCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 146

GCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 170

GCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 62

GCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattact ... tgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACGACGAATCAAATAAACGACAGAAGGTTGATGATGATGTCCAAGAGGGTGCTCTTCCTCCGTATCTGCTGGATCGTGATCAGACACAGCGCGCTAAGgtgaattactgttcttggcttctctccagctaattatgatacagtaacgttttatggcattgatcactgatatctggtgaagtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA