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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgccgtgttcatacatttgactggcgatgaacataaatattatgataaatgatgttgaattgacttcatatacgaatag

Basic information

species Zea mays
transcript GRMZM2G457881_T01
intron # 6
splice site 5'
intron type U12 (go to U12 genes for details)

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|211474511|gb|FK963000.1|FK963000
EST:     TCCATCCTCAAGTATAGATAACTACCATCTGGTTGATGNCTTGGAGTCTC                         ATATATCGAAGGGTGATGAAAATCAACTTGTGCTC
genomic: TCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgcc ... atacgaatagATATATCGAAGGTTGATGAAAATCAACTTGTGCTC
EST: gi|149023564|gb|EE045895.2|EE045895
EST:     TCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTC                         ATATATCGAAGGTTGATGAAAATCAACTTGTGCTCTATGCTCAGATGGCCA
genomic: TCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgcc ... atacgaatagATATATCGAAGGTTGATGAAAATCAACTTGTGCTCTATGCTCAGATGGCCA
EST: gi|211474517|gb|FK963006.1|FK963006
EST:     TCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGCCTTGGAGTCTC                         ATATATCGAAGGGTGAT
genomic: TCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgcc ... atacgaatagATATATCGAAGGTTGAT
EST: gi|211474510|gb|FK962999.1|FK962999
EST:     TCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGCCTTGGAGTCTC                         ATATATCGAAGGGTGATGAAAATCAACT
genomic: TCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgcc ... atacgaatagATATATCGAAGGTTGATGAAAATCAACT
EST: gi|211474507|gb|FK962996.1|FK962996
EST:     TCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGCCTTGGAGTCTC                         ATATATCGAAGGTTGA
genomic: TCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgcc ... atacgaatagATATATCGAAGGTTGA
EST: gi|211474508|gb|FK962997.1|FK962997
EST:     CCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCYC                         ATATATCGAAGGTTGATGAAAATCAAC
genomic: CC-ATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgcc ... atacgaatagATATATCGAAGGTTGATGAAAATCAAC
EST: gi|71322965|gb|DR798157.1|DR798157
EST:     TCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTC                         ATATATCGAAGGTTGATGAAAATCAACTTGTGCTCTATGCTCAGATGGCCA
genomic: TCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgcc ... atacgaatagATATATCGAAGGTTGATGAAAATCAACTTGTGCTCTATGCTCAGATGGCCA
EST: gi|211474509|gb|FK962998.1|FK962998
EST:     TCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGCCTTGGAGTCTC                         ATATATCGAAGGTTGATGAAAATCAACTTGTGC
genomic: TCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgcc ... atacgaatagATATATCGAAGGTTGATGAAAATCAACTTGTGC

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: 24

GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgcc ... atacgaatagATATATCGAAGGTTGATGAAAATCAACTTGTGCTCTATGCTCAGATGGCCAATCTTGTGAGCCTGATTCTTCCTTTTATTGAGCTTGACCTTAAGGAAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 8

GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgcc ... atacgaatagATATATCGAAGGTTGATGAAAATCAACTTGTGCTCTATGCTCAGATGGCCAATCTTGTGAGCCTGATTCTTCCTTTTATTGAGCTTGACCTTAAGGAAAT


Block sizes: 29 (upstream exon), 49 (downstream exon)
Score: 21

GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgcc ... atacgaatagATATATCGAAGGTTGATGAAAATCAACTTGTGCTCTATGCTCAGATGGCCAATCTTGTGAGCCTGATTCTTCCTTTTATTGAGCTTGACCTTAAGGAAAT


Block sizes: 44 (upstream exon), 39 (downstream exon)
Score: 16

GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgcc ... atacgaatagATATATCGAAGGTTGATGAAAATCAACTTGTGCTCTATGCTCAGATGGCCAATCTTGTGAGCCTGATTCTTCCTTTTATTGAGCTTGACCTTAAGGAAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAGTCTCgtatcctgccgtgttcatacatttgactggcgatgaacataaatattatgataaatgatgttgaattgacttcatatacgaatag

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