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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcgccatcctactcagcctcgatgctaattatatgctatcaatgtttatgtgatctgattattggaatcattatttctgtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTCATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG

Basic information

species Zea mays
transcript GRMZM2G068755_T03
intron # 50
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 50
lower sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 51
gtcgccatcctactcagcctcgatgctaattatatgctatcaatgtttatgtgatctgattattggaatcattatttctgtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGT---CATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG
|||  | | ||  |||  || | || |||   |   ||   ||  |||||   |||||||| |  ||||  || ||||| | |||||||| ||||||||||| ||||||||| ||||||||||||||||||| || ||| | |||    ||||||| || | ||||||||| || ||| | || ||      
gtctgccttctg-tcatacttgctgttaagc-tgcacttctaagctttata--atctgattgtatgaattgttctttctatgccagCAGGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCAT------

upper sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 50
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 51
gtcgccatcctactcagcctcgatgctaattatatgctatcaatgtttatgtgatctgattattggaatcattatttctgtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTC---ATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG
|||  | | ||  |||  || | || |||   |   ||   ||  |||||   |||||||| |  ||||  || ||||| | |||||||| ||||||||||| ||||||||| ||||||||||||||||||| || ||| | |||    ||||||| || | ||||||||| || ||| | || |||||   
gtctgccttctg-tcatacttgctgttaagc-tgcacttctaagctttata--atctgattgtatgaattgttctttctatgccagcagGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCATGAA---
















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|78544583|gb|DV622081.1|DV622081
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         GCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
EST: gi|60343345|gb|DN210318.1|DN210318
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         GCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
EST: gi|211309894|gb|FL207376.1|FL207376
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGCAG                       
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCT---CAGgtcgccatcc ... gtaccagc
EST: gi|17930620|gb|BM267580.1|BM267580
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         GCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
EST: gi|211309900|gb|FL207382.1|FL207382
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGCAG                       
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCT---CAGgtcgccatcc ... gtaccagc
EST: gi|78022376|gb|DV490763.1|DV490763
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         GCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
EST: gi|71444353|gb|DR825403.1|DR825403
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         GCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
EST: gi|20512828|gb|BQ280026.1|BQ280026
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         GCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
EST: gi|6095379|gb|AW120046.1|AW120046
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         GCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
EST: gi|71444352|gb|DR825402.1|DR825402
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         GCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTTCAAGCGGCAGCT
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATT-CAAGCGGCAGCT
EST: gi|26456806|gb|CA828389.1|CA828389
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         GCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
EST: gi|60395928|gb|DN228798.1|DN228798
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         GCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTA
EST: gi|211309893|gb|FL207375.1|FL207375
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGCAG                       
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCT---CAGgtcgccatcc ... gtaccagc

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: 136

AAAACAGATTATAACGAAGATAATGCCAGTGGTGAGACACAACCCTTCAGAGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTCATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

AAAACAGATTATAACGAAGATAATGCCAGTGGTGAGACACAACCCTTCAGAGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTCATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

AAAACAGATTATAACGAAGATAATGCCAGTGGTGAGACACAACCCTTCAGAGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTCATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 90

AAAACAGATTATAACGAAGATAATGCCAGTGGTGAGACACAACCCTTCAGAGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... gtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTCATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctatcaatgtttatgtgatctgattattggaatcattatttctgtaccagcagGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTCATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAACGG
                   atctgat  putative branch site (score: 90)
                                        tttctgt  putative PPT
                                aatcattattt  TA-rich tract