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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctacttgtatacttaatcacagagttttatctgttttcttgtcatgtcctcacatttttctgatttttttgtctgctaattgttttctgtattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG

Basic information

species Zea mays
transcript GRMZM2G080652_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|89248438|gb|DY620224.1|DY620224
EST:     TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCCTCGATGGGATTCCTCAGCTCATCTTCGCCAGATCAA
genomic: TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAA
EST: gi|101391113|gb|EB817490.1|EB817490
EST:     TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|211040785|gb|FL108285.1|FL108285
EST:     TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|32837961|gb|CD977639.1|CD977639
EST:     ACAATCAACCTCTCCCAAAAAGATCTCCCTGTNGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: ACAATCAACCTCTCCCAAAAAGATCTCCCTGT-GACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|32823528|gb|CD963250.1|CD963250
EST:     GATCTCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: GATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|32823725|gb|CD963447.1|CD963447
EST:     GATCTCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: GATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|31360794|gb|CD445151.1|CD445151
EST:     TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|78117501|gb|DV535888.1|DV535888
EST:     TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|50325208|gb|CO520334.1|CO520334
EST:     TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGT
genomic: TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGT
EST: gi|71330852|gb|DR802224.1|DR802224
EST:     TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|32823775|gb|CD963497.1|CD963497
EST:     GATCTCCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: GATCT-CCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|71447371|gb|DR828421.1|DR828421
EST:     TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|76294373|gb|DV033941.1|DV033941
EST:     TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|24768059|gb|CA403191.1|CA403191
EST:     CCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: CCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|61119643|gb|DN560604.1|DN560604
EST:     TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAATG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|71330843|gb|DR802223.1|DR802223
EST:     AAAAAGATCTTCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: AAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|101386958|gb|EB815496.1|EB815496
EST:     TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
EST: gi|71309454|gb|DR791014.1|DR791014
EST:     TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTG                         AGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT
genomic: TACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATT

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), 45 (downstream exon)
Score: 82

TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 81

TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 45

TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 105

TTGATGGATATTAACGAAAGCCCTGTTTATCTCCTATTAAATCCTACAATCAACCTCTCCCAAAAAGATCTCCCTGTGACTATCTATGAGAGTGgtaagtcaat ... tattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcctcacatttttctgatttttttgtctgctaattgttttctgtattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG
                             tgctaat  putative branch site (score: 105)
                                      ttttctgt  putative PPT
         atttttctgatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctacttgtatacttaatcacagagttttatctgttttcttgtcatgtcctcacatttttctgatttttttgtctgctaattgttttctgtattttgaagAGTTGCATGTCATCGATGGGATTCCTCAGCTCATCTTCGTCAGATCAAATTATACAATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
-ctacttg
- - - - - - - -aatcaca
- - - - - - - - - - - - - - - tctgttt
- - - - - - - - - - - - - - - - - - - - - -catgtcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtctgct