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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgattctttgattgtccactattcttctggttctctttttagtggaactggctatttcatatgtatacatacatgtaaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGAGTATATGGAATTTCTTTCCCTGATTCTCGACGTCTCACG

Basic information

species Zea mays
transcript GRMZM2G553314_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G553314_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 6
gtaatgattctttgattgtcc-actattcttctggttctctttttagtggaactggctatttcatatgtatacatacatgtaaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGAGTATATGGAATTTCTTTCCCTGATTCTCGACGTCTCACG
    | |||||||| |||||  |   || | || |      ||||  |||||||  | | ||      | ||| | |||||||||||  |||| ||||| || ||||||||||| ||||  || || || ||||||||||||||||||||||||||||| |||||||||  |||||||| |
---gtaattctttggttgtcttaagcttttgcttgccaatatttttatggaactatccaatt------tgtacttgcatgtaaatatgtagGCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGAGTATATGGAATTTCTTTTCCTGATTCTAAACGTCTCAAG
















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|22819104|gb|BU499194.1|BU499194
EST:     GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAG                         GCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
genomic: GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
EST: gi|26457084|gb|CA828667.1|CA828667
EST:     GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAG                         GCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
genomic: GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
EST: gi|87153201|gb|DY397990.1|DY397990
EST:     GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAG                         GCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
genomic: GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
EST: gi|20507213|gb|BQ279533.1|BQ279533
EST:     GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAG                         GCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
genomic: GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
EST: gi|26559163|gb|CA831398.1|CA831398
EST:     GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAG                         GCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
genomic: GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
EST: gi|87157710|gb|DY402499.1|DY402499
EST:     GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAG                         GCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
genomic: GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
EST: gi|22542059|gb|BU092497.1|BU092497
EST:     GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAG                         GCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
genomic: GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
EST: gi|32933378|gb|CF038190.1|CF038190
EST:     GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAG                         GCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
genomic: GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
EST: gi|50334514|gb|CO529640.1|CO529640
EST:     GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAG                         GCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
genomic: GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
EST: gi|19058529|gb|BM737196.1|BM737196
EST:     GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAG                         GCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
genomic: GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
EST: gi|211165966|gb|FL031946.1|FL031946
EST:     GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAG                         GCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
genomic: GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
EST: gi|22490568|gb|BU050491.1|BU050491
EST:     GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAG                         GCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
genomic: GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
EST: gi|9952045|gb|BE638628.1|BE638628
EST:     GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAG                         GCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA
genomic: GGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGA

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: 49 (upstream exon), 48 (downstream exon)
Score: 556

CAAGACCATTACTGTATACAGGTGTGGTCCTTTAGTTGACCTATGCCGTGGGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGAGTATATGGAATTTCTTTCCCTGATTCTCGACGTCTCACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 398

CAAGACCATTACTGTATACAGGTGTGGTCCTTTAGTTGACCTATGCCGTGGGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGAGTATATGGAATTTCTTTCCCTGATTCTCGACGTCTCACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 306

CAAGACCATTACTGTATACAGGTGTGGTCCTTTAGTTGACCTATGCCGTGGGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGAGTATATGGAATTTCTTTCCCTGATTCTCGACGTCTCACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 276

CAAGACCATTACTGTATACAGGTGTGGTCCTTTAGTTGACCTATGCCGTGGGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattc ... aaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGAGTATATGGAATTTCTTTCCCTGATTCTCGACGTCTCACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctttttagtggaactggctatttcatatgtatacatacatgtaaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGAGTATATGGAATTTCTTTCCCTGATTCTCGACGTCTCACG
                     tatttcatatgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgattctttgattgtccactattcttctggttctctttttagtggaactggctatttcatatgtatacatacatgtaaatattcagGCTTCATCATCATATTGGAGAGGAAAAGTTGACCGCGAAAGCCTGCAGAGAGTATATGGAATTTCTTTCCCTGATTCTCGACGTCTCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG