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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatcttcaaaatccttgctgatgaatgagaaattgcaaacaggctcacataagttcgcacattctattgcagAATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT

Basic information

species Zea mays
transcript GRMZM5G875776_T01
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|94473353|gb|EB702311.1|EB702311
EST:     GAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAG                         AATGGGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT
genomic: GAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAGgtgaatcttc ... tctattgcagAATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT
EST: gi|78115891|gb|DV534279.1|DV534279
EST:     GAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAG                         AATGCGAGTTGAATGACAAAAAGAAGCCTCGAGATAACCCACCGCCATCTT
genomic: GAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAGgtgaatcttc ... tctattgcagAATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT
EST: gi|211509969|gb|FL438242.1|FL438242
EST:     GAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAG                         AATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT
genomic: GAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAGgtgaatcttc ... tctattgcagAATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT
EST: gi|211337942|gb|FL007017.1|FL007017
EST:     GAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAG                         AATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT
genomic: GAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAGgtgaatcttc ... tctattgcagAATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT
EST: gi|71429002|gb|DR810052.1|DR810052
EST:     GAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAG                         AATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT
genomic: GAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAGgtgaatcttc ... tctattgcagAATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT
EST: gi|74232722|gb|DT640636.1|DT640636
EST:     GAGCGGTCTATGCAGCAAAGCATCCTTCCACCCTCCTGCTGAAAGTAGAG                         AATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT
genomic: GAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAGgtgaatcttc ... tctattgcagAATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT

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: 38 (upstream exon), 46 (downstream exon)
Score: 20

AACCACCGGTACAAACTTGGCATCAAATAGACGGGGTTACTACTGAGCTGGAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAGgtgaatcttc ... tctattgcagAATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 15

AACCACCGGTACAAACTTGGCATCAAATAGACGGGGTTACTACTGAGCTGGAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAGgtgaatcttc ... tctattgcagAATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 22

AACCACCGGTACAAACTTGGCATCAAATAGACGGGGTTACTACTGAGCTGGAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAGgtgaatcttc ... tctattgcagAATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 26

AACCACCGGTACAAACTTGGCATCAAATAGACGGGGTTACTACTGAGCTGGAGCGGTCTATGCAGCAAAGCATCCTTCCAACCTCCTGCTGAAAGTAGAGgtgaatcttc ... tctattgcagAATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatgaatgagaaattgcaaacaggctcacataagttcgcacattctattgcagAATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT
                        ggctcac  putative branch site (score: 26)
                                            ttctatt  putative PPT
                                           attctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatcttcaaaatccttgctgatgaatgagaaattgcaaacaggctcacataagttcgcacattctattgcagAATGCGAGTTGAATGACAAAAAGAGGCCTCGAGATAACCCACCGCCATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG