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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagttgtcagtgtacatgtctagttggttcgacaaatcgtgtattgaatttccgattcaataagtagatttcgtaaatttgtccggttaacaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCCGACTCCCTATATATCCTCTCATGGATCCAAAGTTGCACGCCTACACATG

Basic information

species Zea mays
transcript GRMZM2G077187_T01
intron # 1
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|76286378|gb|DV025946.1|DV025946
EST:     ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGG                         GACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
genomic: ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
EST: gi|211537297|gb|FK977061.1|FK977061
EST:     ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGG                         GACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
genomic: ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
EST: gi|76935224|gb|DV174245.1|DV174245
EST:     ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGG                         GACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
genomic: ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
EST: gi|61119018|gb|DN559979.1|DN559979
EST:     ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTTTGCCACCGG                         GACTCAAAAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
genomic: ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
EST: gi|78079032|gb|DV507444.1|DV507444
EST:     ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGG                         GACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
genomic: ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
EST: gi|76282158|gb|DV021726.1|DV021726
EST:     ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGG                         GACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
genomic: ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
EST: gi|86467943|gb|DY234313.1|DY234313
EST:     ACCTCGGCGGCGGAAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGG                         GACTCAAGAGGCAATGCCAGCACCACCCCCACCAATTCGTCGGGGACCTCC
genomic: ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
EST: gi|76289091|gb|DV028659.1|DV028659
EST:     ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGG                         GACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
genomic: ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
EST: gi|211537299|gb|FK977063.1|FK977063
EST:     ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGG                         GACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGAC-TCC
genomic: ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
EST: gi|24934529|gb|CA452747.1|CA452747
EST:     ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGG                         GACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC
genomic: ACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCC

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: 40 (upstream exon), 47 (downstream exon)
Score: 11

TTTCTCGCCTCTTCCGCATCTCGAGTTGTCGTGATTAACAAGACAGCAAGACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCCGACTCCCTATATATCCTCTCATGGATCCAAAGTTGCACGCCTACACATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 549

TTTCTCGCCTCTTCCGCATCTCGAGTTGTCGTGATTAACAAGACAGCAAGACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCCGACTCCCTATATATCCTCTCATGGATCCAAAGTTGCACGCCTACACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 667

TTTCTCGCCTCTTCCGCATCTCGAGTTGTCGTGATTAACAAGACAGCAAGACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCCGACTCCCTATATATCCTCTCATGGATCCAAAGTTGCACGCCTACACATG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 29

TTTCTCGCCTCTTCCGCATCTCGAGTTGTCGTGATTAACAAGACAGCAAGACCTCGGCGGCGGCAAACAGTCGAGCACCTGCGAGCGTCTCTGCCACCGGgtatatagct ... acaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCCGACTCCCTATATATCCTCTCATGGATCCAAAGTTGCACGCCTACACATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatttccgattcaataagtagatttcgtaaatttgtccggttaacaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCCGACTCCCTATATATCCTCTCATGGATCCAAAGTTGCACGCCTACACATG
                                        ggttaac  putative branch site (score: 29)
                                          ttaacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagttgtcagtgtacatgtctagttggttcgacaaatcgtgtattgaatttccgattcaataagtagatttcgtaaatttgtccggttaacaatttcagGACTCAAGAGGCAATGCCAGCACCAGCCCCACCAATTCGTCTGGGACCTCCGACTCCCTATATATCCTCTCATGGATCCAAAGTTGCACGCCTACACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - gtacatg
- - - - - - - - - - - - - - - cgacaaa
- - - - - - - - - - - - - - - - - - - - tgtattg