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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatcaattcagcctgcttgttgtttgcaatgaactgcttagctagctatgttgcttacttttgcaatgtcatgtagcttgcaagtgctgattattgttacatcctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG

Basic information

species Zea mays
transcript GRMZM2G143602_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 6
gttatcaattcagcctgcttgttgtttgcaatgaactgcttagctagctatgttgcttacttttgcaatgtcatgtagcttgcaagtgctgattattgttacatcctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG
    | | | | || |   |     |   | ||||||  | |||||| |||||     |   |    | || || |   |||      |||| |     | ||| |     |||||||||||||||||  | ||||||   || |||||||||||| | |||||||||||||| |||||||||||||||||||||||
----tgagtactgcttcagtaaaagtcttattgaact--tgagctagatatgtgataaatcatcttta-gttatttgtgttgtttcc-ctgactccc--tgcattca----cagGTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAG
















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|211466861|gb|FL187159.1|FL187159
EST:     CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
EST: gi|19822196|gb|BQ048220.1|BQ048220
EST:     CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGGACAGATGGGCTGAATGCTTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
EST: gi|21389960|gb|BQ528009.1|BQ528009
EST:     CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGGACAGATGGGCTGAATGCTTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
EST: gi|20507674|gb|BQ279724.1|BQ279724
EST:     CATTTTTCTACGGGCATGGCAACCATGATCAGCTTGTTAAGATAGCCAAG                         GTGCTTGGGACAGATGGGCTGAATGCTTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
EST: gi|6993987|gb|AW453201.1|AW453201
EST:     ATTTTTCTACGGGCATGACAACCATGATCAACTTGCTAAGATAGCCAAG                         GTACTTGGGACAGATGGGCTGAATGCTTATTTGAACAAGTACAGAATTGAG
genomic: ATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
EST: gi|60348663|gb|DN215636.1|DN215636
EST:     CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
genomic: CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAG
EST: gi|71770653|gb|DR968590.1|DR968590
EST:     CATTTTTCTACGGGCATGACAACTATGATCAACTTGTTAAGATAGCCAAG                         GTACTTGGGACAGATGGGCTGAATG
genomic: CATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATG

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: 538

ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 332

ATTTTTCGTAAGGAACCATTTTTCTACGGGCATGACAACCATGATCAACTTGTTAAGATAGCCAAGgttatcaatt ... cctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgcaatgtcatgtagcttgcaagtgctgattattgttacatcctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG
                           tgctgat  putative branch site (score: 332)
                                            tcctttatc  putative PPT
                                attattgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatcaattcagcctgcttgttgtttgcaatgaactgcttagctagctatgttgcttacttttgcaatgtcatgtagcttgcaagtgctgattattgttacatcctttatcagGTACTTGGGACAGATGGGCTGAATGTTTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTTGAAGCCCTCGTTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG