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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgcatatgttcacatgaaaggattgttataaattaaagagagtagatgtggagacttttgggacctctccatccaatacctgatatctgaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG

Basic information

species Zea mays
transcript GRMZM2G071620_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|78104752|gb|DV523170.1|DV523170
EST:     TCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
genomic: TCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|148980769|gb|EE027337.2|EE027337
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAAGT-GAGGTTTTACA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGA-GTTGAGGTTTTACA
EST: gi|78104753|gb|DV523171.1|DV523171
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|21331630|gb|BQ487011.1|BQ487011
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTTCCATCTTGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|78085639|gb|DV514032.1|DV514032
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|31909804|gb|CD651102.1|CD651102
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|71436647|gb|DR817697.1|DR817697
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|50326015|gb|CO521141.1|CO521141
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|211530058|gb|FL388005.1|FL388005
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|71448410|gb|DR829460.1|DR829460
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|101383824|gb|EB813967.1|EB813967
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|93016628|gb|EB642148.1|EB642148
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGGTTTACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|71436011|gb|DR817061.1|DR817061
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTT-ACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|50325855|gb|CO520981.1|CO520981
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|211467003|gb|FL313839.1|FL313839
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTG
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTG
EST: gi|30031661|gb|CB833512.1|CB833512
EST:     ACATCTATGCTTCAGCTGATGGTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTGTTACA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTT-TTACA
EST: gi|76285216|gb|DV024784.1|DV024784
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
EST: gi|32836421|gb|CD976099.1|CD976099
EST:     ACATCTATGCTTCAGCTGATGCTGCAGTTCCATCTTGCGATGAGATGCAG                         AATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA
genomic: ACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAA

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 16

TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAGgtgcgcggac ... gaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgtggagacttttgggacctctccatccaatacctgatatctgaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG
                                  acctgat  putative branch site (score: 16)
                                            tgaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgcatatgttcacatgaaaggattgttataaattaaagagagtagatgtggagacttttgggacctctccatccaatacctgatatctgaaaatgcagAATAACTATCAAGAATATGTGAAGCTGAAAGCACGAGTTGAGGTTTTACAACACTCGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
-atgcata
- - - - - - - catgaaa
- - - - - - - - - - - - - - - - - - aaagagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacctg