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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgctgcacattcaggtcatacctatggtatcttgattgcagtttttgttgcacatatatttacctagtttatggccaccaatgcctggctaaatcctctcccgaaaatagaggttctgaatcctgaatttgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCAGAGCATGTTGACAATGGCTTCCTGCACAGGTCAGAGGTAACCCGAGAGG

Basic information

species Zea mays
transcript GRMZM2G068392_T01
intron # 3
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|78076514|gb|DV504948.1|DV504948
EST:     GAAGAGAGGGCAGTACGCTGCTTTTCAA-GATGAGTTCCTTACCAACCCT                         GTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
genomic: GAAGAGAGGGCAGTACGCTGCTTT-CAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
EST: gi|148935027|gb|EC879068.2|EC879068
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGT                        
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC--Tgtaagtcgct ... tgctaggta
EST: gi|148935027|gb|EC879068.2|EC879068
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGT                        
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC--Tgtaagtcgct ... tgctaggta
EST: gi|148935027|gb|EC879068.2|EC879068
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTGT                        
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCC--Tgtaagtcgct ... tgctaggta
EST: gi|211170268|gb|FL097997.1|FL097997
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         GTAGAAAGAGCGC
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGC
EST: gi|71433967|gb|DR815017.1|DR815017
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         GTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
EST: gi|211170254|gb|FL097983.1|FL097983
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         GTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
EST: gi|50324142|gb|CO519268.1|CO519268
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         GTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
EST: gi|50331565|gb|CO526691.1|CO526691
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         GTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
EST: gi|38502614|gb|CF972474.1|CF972474
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         GTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
EST: gi|211166904|gb|FL097963.1|FL097963
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         GTAGAAAGAGCGCAAACAGGTGCCAACAGAAGG
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGCAA-CAGGTGCCAACAGAAGG
EST: gi|50331308|gb|CO526434.1|CO526434
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         GTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
EST: gi|44681890|gb|CK786938.1|CK786938
EST:     AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCT                         GTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA
genomic: AGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCA

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: 100

ACTGGGCTATCTGCCCAATGACCGCTCGCTGTGGGAGCAGGAGCTGGCAAAGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCAGAGCATGTTGACAATGGCTTCCTGCACAGGTCAGAGGTAACCCGAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

ACTGGGCTATCTGCCCAATGACCGCTCGCTGTGGGAGCAGGAGCTGGCAAAGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCAGAGCATGTTGACAATGGCTTCCTGCACAGGTCAGAGGTAACCCGAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

ACTGGGCTATCTGCCCAATGACCGCTCGCTGTGGGAGCAGGAGCTGGCAAAGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCAGAGCATGTTGACAATGGCTTCCTGCACAGGTCAGAGGTAACCCGAGAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 88

ACTGGGCTATCTGCCCAATGACCGCTCGCTGTGGGAGCAGGAGCTGGCAAAGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgct ... tgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCAGAGCATGTTGACAATGGCTTCCTGCACAGGTCAGAGGTAACCCGAGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggctaaatcctctcccgaaaatagaggttctgaatcctgaatttgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCAGAGCATGTTGACAATGGCTTCCTGCACAGGTCAGAGGTAACCCGAGAGG
  ggctaaa  putative branch site (score: 88)
                   aaaataga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcgctgcacattcaggtcatacctatggtatcttgattgcagtttttgttgcacatatatttacctagtttatggccaccaatgcctggctaaatcctctcccgaaaatagaggttctgaatcctgaatttgctaggtagGTAGAAAGAGCGCAACAGGTGCCAACAGAAGGCCACCACAACGTAAGTGCAGAGCATGTTGACAATGGCTTCCTGCACAGGTCAGAGGTAACCCGAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG