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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcaacctatcatgaataaattgaaatattggtggcatgtgactctttgtgccctaataaaaaaatccaagtattaggatttaacatactttcttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTG

Basic information

species Zea mays
transcript GRMZM2G051050_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g38950.2 (Oryza sativa), 3'ss of exon 8
gttagcaacctatcatgaataaattgaaatattggtggcatgtgactctttgtgcc--ctaataaaaaaatccaagtattaggatttaacatactttcttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTG
||| ||||| |||    ||||   ||| |||||||||    ||| ||| ||  ||     | |  ||||||  ||  ||||  |  | |  | |||| |||  |||||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||| ||||||| ||||| ||||||||||||||||| ||||
gttcgcaacttattgcaaata---tgatatattggtgtggcgtgcctcatttagctagtaacttcaaaaatataataattaaaagctgatttccttttttg-tgcagCAAATCACCTGGATTACCTTGGTCTTCAAGTTGCATGGGTTACTGGACCATGGTTCCTATCCATTTTCACCAATGTGCTTCCTTGGGAGAGTG

upper sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 8
gttagcaacctatcatgaataaattgaaatattgg---tggcatgtgactctttgtgccctaataaaaaaatccaagtattaggatttaacatactttcttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTG
||| | || ||||  | | | | ||     ||||       ||  |||   ||  | |     | | |      |  | |||   | |    | |  | ||   ||||| ||||| || ||||| || ||| | || || |||||||||||||| ||||||||| | ||||| ||   |||  ||||||||||||||||||
gtttgtaaactattttaattcatttttgtcattgaacccaccaactgaaatttgtttctagtgtcacatttcttacttgttattttcttgtgttcactttttttgcagCCAATCATCTAGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG

upper sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 8
gttagcaacctatcatgaataaattgaaatattggtggcat---gtgactctttgtgccctaataaaaaaatccaagtattag--gatttaacatactttcttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTG
||| | || ||||  | | | | ||      |||    ||    |||| | ||  | |    ||   |      |  | |||    |||    ||||||  ||   ||||| ||||| |||||||| || ||| | || || |||||||||||||| ||||||||| | ||||| ||   |||  ||||||||||||||||||
gtttgtaaactattttaattcatttttgtctttgaactcacaaagtgaattttgtttctagcattccatttcttatttgttatttaattgtgtatacttattt--tgcagCCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG

upper sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 8
gttagcaacctatcatgaataaattgaaatattggtggcatgtgactctttgtgccctaataaaaaaatccaagtattaggatttaacatactttcttgac-gcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTG
               ||| |    | |||     ||    |||  |   ||||    |  | | |       |||| || | | |   |   ||   || |  |||   |||| |||||||| |||||| | ||||| || |||||||| |||||||||||  | |||||||||| |||| ||||||| ||||||||||
--------------gtgagttccctcaaa-----gttttttgtttcatcttgtagaatgttcacag----ttagtactaagctctgcaacttttctatgtctacagTTCATCATCTGGATTATCTTGGAGTGCAAGTGGCTTGGGTTACAGGGCCATGGTTTCTTTCCATCTTCATGAATATGCTTCCATGGGAAAGTG

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|87152631|gb|DY397420.1|DY397420
EST:     TCGAGAGAAGTTCCCTAAATTAG                         CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCAT
genomic: TCGAGAGAAGTTCCCTAAATTAGgttagcaacc ... cttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCAT
EST: gi|32851391|gb|CD991072.1|CD991072
EST:     GGACCAGCTTGTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAG                         CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCAT
genomic: GGACCAGCTTGTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAGgttagcaacc ... cttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCAT
EST: gi|19058398|gb|BM737065.1|BM737065
EST:     CCCTAAATTAG                         CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCAT
genomic: CCCTAAATTAGgttagcaacc ... cttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCAT
EST: gi|22490585|gb|BU050508.1|BU050508
EST:     GCTTGTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAG                         CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCAT
genomic: GCTTGTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAGgttagcaacc ... cttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCAT
EST: gi|32851141|gb|CD990822.1|CD990822
EST:     GGACCAGCTTGTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAG                         CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCAT
genomic: GGACCAGCTTGTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAGgttagcaacc ... cttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCAT
EST: gi|32834207|gb|CD973885.1|CD973885
EST:     GGACCAGCTTGTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAG                         CAAATCACCTGGATTACCTTGGA
genomic: GGACCAGCTTGTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAGgttagcaacc ... cttgacgcagCAAATCACCTGGATTACCTTGGA
EST: gi|19057887|gb|BM736554.1|BM736554
EST:     GTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAG                         CAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCAT
genomic: GTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAGgttagcaacc ... cttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCAT

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: 105

GTGGACCAGCTTGTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAGgttagcaacc ... cttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 61

GTGGACCAGCTTGTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAGgttagcaacc ... cttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 43

GTGGACCAGCTTGTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAGgttagcaacc ... cttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 95

GTGGACCAGCTTGTTTTAGAGGAGTTAGTTCGAGAGAAGTTCCCTAAATTAGgttagcaacc ... cttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgccctaataaaaaaatccaagtattaggatttaacatactttcttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTG
                                            tcttgac  putative branch site (score: 95)
                                       tactttctt  CT-rich tract
       taataaaaaaatccaa  TA-rich tract