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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaagactactactagaagtcgagaacattgtagccttagagttctcacttcatttccatttcatatgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA

Basic information

species Zea mays
transcript GRMZM2G079236_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079236_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g25310.2 (Oryza sativa), 3'ss of exon 9
gtaagtaagactactactagaagtcgagaacattgtagccttagagttctcacttca-tttccatttcatatgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
||||  | ||    | | |    ||        |  |     | | || |||||||| |||   ||||  || ||   ||||| || |||||||| || |||||||| |||||||| ||||||||||||||||||||||| |||||||| ||||| ||||| || ||||| ||||||||||
gtaa--aggatctttgccaatcatccttggtggtcaaatacaatatttttcacttcaatttttgtttctgattactc-cagGTAGATGAGAGGGGAATGCGCTGGTTTTACACTGGAGATATTGGCCAGTTCCATCCTGATGGGTGCCTCGAGATCATTGATAGAAAAAAGGATATAGTAA

upper sequence: GRMZM2G079236_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G11700.1 (Glycine max), 3'ss of exon 9
-------------------------------------------gtaagtaagacta--ctactagaagtcgagaacattgtagccttagagttctcacttcatttccatttcatatgacc-tacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
                                            ||| |     ||   |      | |           ||    ||     ||   | |||||   |||  ||      |||||||||| |||| ||| || |||||||| || ||||| |||||||| || ||||||||||| || || ||||| || || || ||||| |||||||| || |
gtaatttccaaacttatagttgtatgcatgccatttttcctttataatttcctttaatttctctttaatttgcttttgcatattactaagacacttgttacatttttgttttttaacttagtacagGTTGATGAGAAGGGAATGCGCTGGTTTTATACTGGCGATATTGGGCAATTCCATCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA

upper sequence: GRMZM2G079236_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA20G07280.1 (Glycine max), 3'ss of exon 8
-----------------------------------------------gtaagtaagactactactaga---agtcgagaacattgtagccttagagttctcacttcatttccatttcatatgacc-tacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
                                                |   |   ||| ||  || |     |   | | |||        |    |  || ||  |||   |||  ||      |||||||||| ||||  ||||| |||||||| || |||||||||||||| || ||||| ||||| || || ||||| || || || ||||| |||||||| || |
gtaatttcccaagttacagttgtatgcatgacatttttcctttttaatttcctttaactgctcttaaatctgtttttgcatattactaagccactcgttacattttttttttgttttttaacttagtacagGTTGATGAGAAAGGTATGCGCTGGTTTTATACTGGTGATATTGGGCAATTCCACCCTGATGGATGTCTTGAAATCATAGATAGGAAGAAAGATATTGTCA

upper sequence: GRMZM2G079236_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv12s0057g01270.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------------------------------------------------------------gtaagtaagac---tactactagaagtcgag-aacattgtagccttagagttctcacttcatttccatttcatatgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
                                                                                                     ||   || ||   ||    |     | | | |||| |  | | |  || |     | |   |  ||| || | ||  ||||||||||| |||||||| || |||||||| || |||||||| ||||| ||||| || ||| | || |||||||| || ||||||||||| || ||||| || |
gtaataagtaacttcttttgtggataggtgcctgtattggcatttgtatttactttttgtgtatttatatatatatatatgtgtgtgtatgtatatatacatacacaatacatatatactttcttatagtgcaacacttcaacttgtgaatagctgcgttggtgacatatcgtctg--ctacagGTTGATGAGAGGGGCATGCGCTGGTTTTATACTGGTGACATTGGACAGTTTCAACCTAATGGTTGCCTTGAAATAATTGACAGGAAGAAGGATATTGTTA

upper sequence: GRMZM2G079236_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ26722 (Selaginella moellendorffii), 3'ss of exon 8
gtaagtaagactactactagaagtcgagaacattgtagccttagagttctcac-ttcatttccatttcatatgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
                        | |       ||  ||||  ||   |||  || | |||  |||  | |||     |||||||||||||||| ||  | ||||||||||||||||| ||||| || |||||||| || || ||| | || ||| | ||| |||| || || || || |
---------------------gtacaacttttcagtttccttgaagcgttcatgtttaattcgtttttttgtga-----agGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTCCATCCCGATGGTTGCTTAGAAATTGTAGACCGGAAGAAGGACATTGTTA

upper sequence: GRMZM2G079236_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ27012 (Selaginella moellendorffii), 3'ss of exon 8
gtaagtaagactactactagaagtcgagaacattgtagccttagagttctcacttcatttccatttcatatgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
                 || || |    |   |  | |    || ||||   ||| |||    |||  | |||     |||||||||||||||| ||  | ||||||||||||||||| ||||| ||||||||||| || || ||||| || ||| | ||| |||| || || || || |
----------------gtacaacttttcagtttccttga---agcgttcatgcttaattgggtttttttgtga-----agGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTCCATCCCGATGGTTGCCTGGAAATTGTAGACCGGAAGAAGGACATTGTTA

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|211459497|gb|FL315578.1|FL315578
EST:     TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAG                         GTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTC
genomic: TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTC
EST: gi|211220660|gb|FL342324.1|FL342324
EST:     TAACAMAASGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACMAG                         GTTGACGAGAGGGGTATACGC
genomic: TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGC
EST: gi|211234597|gb|FL315442.1|FL315442
EST:     TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAG                         GTTGACGAGAGGGGCATACGCTGGTTCTACACTGGTGATATTGGCCAGTTC
genomic: TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTC
EST: gi|211396222|gb|FL320944.1|FL320944
EST:     TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAG                         GTTGACGAGAGGGGTATACGCTG
genomic: TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGCTG
EST: gi|211281066|gb|FL309975.1|FL309975
EST:     TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAG                         GTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTC
genomic: TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTC
EST: gi|67024251|gb|CO453000.1|CO453000
EST:     TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAG                         GTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTC
genomic: TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTC
EST: gi|211514853|gb|FL332912.1|FL332912
EST:     TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAG                         GTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATT
genomic: TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATT
EST: gi|211218465|gb|FL333878.1|FL333878
EST:     TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAG                         GTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGG
genomic: TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGG
EST: gi|32838733|gb|CD978414.1|CD978414
EST:     TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAG                         GTTGACGAGAGGGGCATACGCTGG
genomic: TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGCTGG
EST: gi|211067389|gb|FL344088.1|FL344088
EST:     TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAG                         GTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTC
genomic: TAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTC

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: 47 (upstream exon), 49 (downstream exon)
Score: 357

TTCTGATTATCCGATGCCGAGAGGAGAGGTCGTGGTTGGCGGACACAGTATAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 588

TTCTGATTATCCGATGCCGAGAGGAGAGGTCGTGGTTGGCGGACACAGTATAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 460

TTCTGATTATCCGATGCCGAGAGGAGAGGTCGTGGTTGGCGGACACAGTATAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 850

TTCTGATTATCCGATGCCGAGAGGAGAGGTCGTGGTTGGCGGACACAGTATAACAAAAGGCTATTTCAGCAATGAAGCAAAGACGAATGAAGTATACAAGgtaagtaaga ... tgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaacattgtagccttagagttctcacttcatttccatttcatatgacctacagGTTGACGAGAGGGGTATACGCTGGTTCTACACTGGTGATATTGGCCAGTTCCATCCTGACGGGTGCCTTGAGATTATTGACAGGAAAAAAGATATAGTAA
                     ttctcac  putative branch site (score: 850)
                                     atttcatat  TA-rich tract