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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggatctcgcctacaaaccgagcaacaccctcccatttctctctttgctcgctcaagtgcttctgatacatccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACCCGGTGGAGTACCTGGTGTCTTACAGGAAGGGCGGGCCGTCGTTCGGCTC

Basic information

species Zea mays
transcript GRMZM2G143651_T01
intron # 11
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|30031664|gb|CB833515.1|CB833515
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|18164602|gb|BM334441.1|BM334441
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|16927071|gb|BM080140.1|BM080140
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|29545100|gb|CB605278.1|CB605278
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|211264901|gb|FK979901.1|FK979901
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTATCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCARAAGCT-AAAGGGGTAC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGG-TAC
EST: gi|60397747|gb|DN230563.1|DN230563
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTATCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCT-AAAGGGGTAC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGG-TAC
EST: gi|67015444|gb|CO444193.1|CO444193
EST:     CCTAGACCAAAT-AACGCATTTGCTGTGGACA-CCTCGTATCGGAAGA-G                         CTCTGACTTTCGA
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGA
EST: gi|211264900|gb|FK979900.1|FK979900
EST:     CTAGACCAAATCAACGCATTTTGCTGTGGACAACCTCGTATCGGAAGATG                         CTCTGACTTTCAAAGACCTCAGCATCATGCCTCAGAAGCT-AAAG
genomic: CTAGACCAAATCAACGCATTT-GCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAG
EST: gi|120480121|gb|EH210746.1|EH210746
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|30087962|gb|CB886167.1|CB886167
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|71445607|gb|DR826657.1|DR826657
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|211383681|gb|FL229452.1|FL229452
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|31612342|gb|CD568964.1|CD568964
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|149069993|gb|EE158393.2|EE158393
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|211418862|gb|FL076974.1|FL076974
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTTGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|31664373|gb|CD573098.1|CD573098
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|149064146|gb|EE286442.2|EE286442
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|31998441|gb|CD662076.1|CD662076
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
EST: gi|4886142|gb|AI677262.1|AI677262
EST:     CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATG                         CTCTGACTTTTGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC
genomic: CCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACC

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: 49 (upstream exon), 47 (downstream exon)
Score: 295

ATGCTGCTCAATAAAGTGCCGTTCCCGCTTCCAACACCATCCATTTTCAACCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACCCGGTGGAGTACCTGGTGTCTTACAGGAAGGGCGGGCCGTCGTTCGGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 462

ATGCTGCTCAATAAAGTGCCGTTCCCGCTTCCAACACCATCCATTTTCAACCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACCCGGTGGAGTACCTGGTGTCTTACAGGAAGGGCGGGCCGTCGTTCGGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 547

ATGCTGCTCAATAAAGTGCCGTTCCCGCTTCCAACACCATCCATTTTCAACCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACCCGGTGGAGTACCTGGTGTCTTACAGGAAGGGCGGGCCGTCGTTCGGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 358

ATGCTGCTCAATAAAGTGCCGTTCCCGCTTCCAACACCATCCATTTTCAACCTAGACCAAATCAACGCATTTGCTGTGGACAACCTCGTCTCGGAAGATGgtgaggatct ... ccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACCCGGTGGAGTACCTGGTGTCTTACAGGAAGGGCGGGCCGTCGTTCGGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accctcccatttctctctttgctcgctcaagtgcttctgatacatccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACCCGGTGGAGTACCTGGTGTCTTACAGGAAGGGCGGGCCGTCGTTCGGCTC
                                  ttctgat  putative branch site (score: 358)
                                          catccctct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggatctcgcctacaaaccgagcaacaccctcccatttctctctttgctcgctcaagtgcttctgatacatccctctgcagCTCTGACTTTCGAAGACCTCAGCATCATGCCTCAGAAGCTGAAAGGGTACCCGGTGGAGTACCTGGTGTCTTACAGGAAGGGCGGGCCGTCGTTCGGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG