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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaatttatggaaattcttgcttttgtaggttctatgcatacatgtacaactttagatggttaagctaaagagttatatgcgctaaacgtttcttgta...

Basic information

species Zea mays
transcript GRMZM2G344476_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G344476_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g47120.1 (Oryza sativa), 5'ss of exon 3
AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgta-aaatttatggaaattcttgcttttgtaggttctatgcatacatgtacaactttagatggttaagctaaagagttatatgcgctaaac--gtttcttgta
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AACCTGGTGGTTACGTTGCTCGTGAAGGTGACCCTGTAGATGGCCTTTACATCATATTGGATGGGCAGgtatgaattggagtatattatttctttgcttagcatt-tattggcttttatgattacc-atactttgggaacaaatatgcaagctgtcatttagccagttgt-
















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|50337659|gb|CO532785.1|CO532785
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|148956464|gb|EC902291.2|EC902291
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|74238643|gb|DT646557.1|DT646557
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|211119071|gb|FL021982.1|FL021982
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|149104205|gb|EE289638.2|EE289638
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|148936448|gb|EC880552.2|EC880552
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|149112589|gb|EE191373.2|EE191373
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|91872284|gb|EB402241.1|EB402241
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|71315516|gb|DR794364.1|DR794364
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|50331303|gb|CO526429.1|CO526429
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|148958992|gb|EE010517.2|EE010517
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|148944150|gb|EC889238.2|EC889238
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|4730512|gb|AI649678.1|AI649678
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|71315960|gb|DR794668.1|DR794668
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
EST: gi|91875931|gb|EB405888.1|EB405888
EST:     CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG                         GCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT
genomic: CTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTAT

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: 44 (upstream exon), 49 (downstream exon)
Score: 36

AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 85

AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 60

AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 76

AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaattta ... tatcctgaagGCTGAAGTTTCTGCACCTGCGAATGCAGAAGAAGCAAATCGCCCAGACTATGTGTTAAATAAGTACGACTACTTTGGTTATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAGgtaaaatttatggaaattcttgcttttgtaggttctatgcatacatgtacaactttagatggttaagctaaagagttatatgcgctaaacgtttcttgta

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA