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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgccgccgtcggtgctctgcttctcccccaccggcctccacataatcgtcctttttcccttccgatttttcaccaactgaaggagttgttgtcttgttgaaactgctggtgctgggttgtgggttgcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG

Basic information

species Zea mays
transcript GRMZM5G892742_T04
intron # 2
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|22472922|gb|BU037402.1|BU037402
EST:     CCCCGTCCCCATCTCATGCCCCACCTGTCTCCCCATCCAAATG                         AAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTACGNG-GGCAGTTAC
genomic: CCCCGTCCCCATCTCATGCCCCACC-GTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATG-GTGGCAGTTAC
EST: gi|101401378|gb|EB822366.1|EB822366
EST:     CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATG                         AAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
genomic: CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
EST: gi|71439824|gb|DR820874.1|DR820874
EST:     CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATG                         AAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
genomic: CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
EST: gi|71438689|gb|DR819739.1|DR819739
EST:     CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATG                         AAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
genomic: CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
EST: gi|87155688|gb|DY400477.1|DY400477
EST:     CCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATG                         AAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTACGGTGGCAGTTACC
genomic: CCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
EST: gi|148999746|gb|EE036749.2|EE036749
EST:     CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAAT-                         --GGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
genomic: CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
EST: gi|71438626|gb|DR819676.1|DR819676
EST:     CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATG                         AAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
genomic: CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
EST: gi|71422780|gb|DR805839.1|DR805839
EST:     CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATG                         AAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
genomic: CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
EST: gi|211426297|gb|FL054605.1|FL054605
EST:     CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATG                         AAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
genomic: CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
EST: gi|76014459|gb|DT941629.1|DT941629
EST:     CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATG                         AAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
genomic: CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
EST: gi|71446190|gb|DR827240.1|DR827240
EST:     CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATG                         AAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
genomic: CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
EST: gi|76285537|gb|DV025105.1|DV025105
EST:     CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATG                         AAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
genomic: CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
EST: gi|101387480|gb|EB815755.1|EB815755
EST:     CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATG                         AAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC
genomic: CATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACC

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: 48 (upstream exon), 48 (downstream exon)
Score: 65

CCTCCCAACGGCGACAACGCCTATGCTTACCCGCCGTCCATTCATAGCGCCATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 114

CCTCCCAACGGCGACAACGCCTATGCTTACCCGCCGTCCATTCATAGCGCCATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 139

CCTCCCAACGGCGACAACGCCTATGCTTACCCGCCGTCCATTCATAGCGCCATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 167

CCTCCCAACGGCGACAACGCCTATGCTTACCCGCCGTCCATTCATAGCGCCATGCTCTCCCCGTCCCCATCTCATGCCCCACCGTCTCCCCATCCAAATGgtaatttgcc ... gcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgccgccgtcggtgctctgcttctcccccaccggcctccacataatcgtcctttttcccttccgatttttcaccaactgaaggagttgttgtcttgttgaaactgctggtgctgggttgtgggttgcatctgcagAAGGGTTGGCGATTGTTCCTCAAGGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG