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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtttgtttatcggtcattttatgtacttttcttcgtctgtttttttcctgttgaacaaccaatgttttcaatggaaaaatgtattttgatgatgtggaatgaaaatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGTTACTCTGCTGTAGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGT

Basic information

species Zea mays
transcript GRMZM2G165817_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165817_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g10640.1 (Oryza sativa), 3'ss of exon 3
gtgtgtttgtttatcggtcattttatgtacttttc-ttcgtctgttttt-------ttcctgttgaacaaccaatgttttcaatggaaaaatgtattttgatgatgtggaatgaaaat-------ccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGTTACTCTGCTGTAGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGT
|| | |||  || |     ||  | |    ||||| || |    |||||        |  |  || |  | |||| |||| ||   ||||  |    |    ||| |  ||      |       |||||||||||| |||||||| || ||||||||||||||||| || || |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
gtatatttagtttttaaaaatcatcttcctttttcattggagcatttttgtcgaaccttttactgtaggagcaatttttttaaacaaaaatcgatgatctgggatttaaaactgcttttttccccccttcagGTGGACCCTGTGGTTTACAACATGCTTCATGAAGACCCTGGTAATGTCAGTTACTCTGCTGTTGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGT
















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|211241231|gb|FL076775.1|FL076775
EST:     TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAG                         GTGGATCCTGTGGTATATAACATGCTTTCATGAAGAT
genomic: TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTT-CATGAAGAT
EST: gi|19822398|gb|BQ048422.1|BQ048422
EST:     TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAG                         GTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGT
genomic: TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGT
EST: gi|60400478|gb|DN233285.1|DN233285
EST:     TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAG                         GTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGT
genomic: TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGT
EST: gi|211238994|gb|FL076765.1|FL076765
EST:     TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAG                         GTGGATCCTGTGGTATATAACATGCTTCATGAAGAT
genomic: TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGAT
EST: gi|22472946|gb|BU037426.1|BU037426
EST:     TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAG                         GTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGT
genomic: TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGT
EST: gi|15499352|gb|BI595865.1|BI595865
EST:     TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAG                         GTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGT
genomic: TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGT
EST: gi|211239003|gb|FL076774.1|FL076774
EST:     TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAG                         GTGGATCCTGTGGTATA
genomic: TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATA
EST: gi|211243473|gb|FL076795.1|FL076795
EST:     TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAG                         GTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAA-TGTCAGT
genomic: TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGT
EST: gi|211243469|gb|FL076791.1|FL076791
EST:     TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAG                         GTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGA
genomic: TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGA
EST: gi|211236768|gb|FL076759.1|FL076759
EST:     TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAG                         GTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGGAAATGTCAG
genomic: TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGG-AAATGTCAG
EST: gi|148950536|gb|EC896111.2|EC896111
EST:     TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAG                         GTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGT
genomic: TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGT
EST: gi|211238993|gb|FL076764.1|FL076764
EST:     TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAG                         GTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGT
genomic: TTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGT

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), 49 (downstream exon)
Score: 425

CGGTTGCCGAAGTAAAGTGGACAAGGAGAAGTTGACATCTGGTACTCGTGTTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGTTACTCTGCTGTAGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 318

CGGTTGCCGAAGTAAAGTGGACAAGGAGAAGTTGACATCTGGTACTCGTGTTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGTTACTCTGCTGTAGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 293

CGGTTGCCGAAGTAAAGTGGACAAGGAGAAGTTGACATCTGGTACTCGTGTTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGTTACTCTGCTGTAGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 311

CGGTTGCCGAAGTAAAGTGGACAAGGAGAAGTTGACATCTGGTACTCGTGTTGTACTTGACATGACGACCTTGACAATAATGCGCACTCTTCCACGGGAGgtgtgtttgt ... aatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGTTACTCTGCTGTAGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaatgttttcaatggaaaaatgtattttgatgatgtggaatgaaaatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGTTACTCTGCTGTAGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGT
                         ttttgat  putative branch site (score: 311)
                                               tccttc  putative PPT
                aaaaatgtattttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtttgtttatcggtcattttatgtacttttcttcgtctgtttttttcctgttgaacaaccaatgttttcaatggaaaaatgtattttgatgatgtggaatgaaaatccttcagGTGGATCCTGTGGTATATAACATGCTTCATGAAGATCCAGGAAATGTCAGTTACTCTGCTGTAGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA