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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcgccatcctactcagcctcgatgctaattatatgctatcaatgtttatgtgatctgattattggaatcattatttctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTCATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAA

Basic information

species Zea mays
transcript GRMZM2G068755_T01
intron # 52
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 52
lower sequence: LOC_Os01g60040.1 (Oryza sativa), 3'ss of exon 51
gtcgccatcctactcagcctcgatgctaattatatgctatcaatgtttatgtgatctgattattggaatcattatttctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGT---CATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAA
|||  | | ||  |||  || | || |||   |   ||   ||  |||||   |||||||| |  ||||  || ||||| | |||||||| ||||||||||| ||||||||| ||||||||||||||||||| || ||| | |||    ||||||| || | ||||||||| || ||| | || ||   
gtctgccttctg-tcatacttgctgttaagc-tgcacttctaagctttata--atctgattgtatgaattgttctttctatgccagCAGGGACGTTGGATGCCCTTAGGGAACGGATGAAAAGCATTCAAGCTGCTGCTGTTGGTGCCAATTTTGATGGAGTTCAGGCTCGTCCATTGCCGAGCAT---

upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 52
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 51
gtcgccatcctactcagcctcgatgctaattatatgctatcaatgtttatgtgatctgattattggaatcattatttctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTC---ATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAA
|||  | | ||  |||  || | || |||   |   ||   ||  |||||   |||||||| |  ||||  || ||||| | |||||||| ||||||||||| ||||||||| ||||||||||||||||||| || ||| | |||    ||||||| || | ||||||||| || ||| | || |||||
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|6095379|gb|AW120046.1|AW120046
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         --G-CACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
EST: gi|78544583|gb|DV622081.1|DV622081
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCT---                         CAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
EST: gi|26456806|gb|CA828389.1|CA828389
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         --G-CACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
EST: gi|20512828|gb|BQ280026.1|BQ280026
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         --G-CACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
EST: gi|60343345|gb|DN210318.1|DN210318
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCT---                         CAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
EST: gi|211309893|gb|FL207375.1|FL207375
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         CAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
EST: gi|211309900|gb|FL207382.1|FL207382
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         CAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
EST: gi|71444352|gb|DR825402.1|DR825402
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         --G-CACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTTCAAGCGGCA
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATT-CAAGCGGCA
EST: gi|17930620|gb|BM267580.1|BM267580
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCT---                         CAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
EST: gi|60395928|gb|DN228798.1|DN228798
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         --G-CACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
EST: gi|211309894|gb|FL207376.1|FL207376
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         CAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
EST: gi|71444353|gb|DR825403.1|DR825403
EST:     AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAG                         --G-CACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG
genomic: AGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAG

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: 39 (upstream exon), 49 (downstream exon)
Score: 24

AAAACAGATTATAACGAAGATAATGCCAGTGGTGAGACACAACCCTTCAGAGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTCATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 33

AAAACAGATTATAACGAAGATAATGCCAGTGGTGAGACACAACCCTTCAGAGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTCATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 31

AAAACAGATTATAACGAAGATAATGCCAGTGGTGAGACACAACCCTTCAGAGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTCATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 24

AAAACAGATTATAACGAAGATAATGCCAGTGGTGAGACACAACCCTTCAGAGGTCAAGGTGCCATCACCGACCAACAAACTGATAGATACCATACCTCAGgtcgccatcc ... tctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTCATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgctatcaatgtttatgtgatctgattattggaatcattatttctgtaccagCAGGCACGTTGGATGCTCTTAGGGAAAGGATGAAAAGCATTCAAGCGGCAGCTATAGGTCATTTTGACGGTGCTCAGGCTCGGCCGTTGGCAAGTATGAA
                      atctgat  putative branch site (score: 24)
                                        ttatttct  putative PPT
                                   aatcattattt  TA-rich tract