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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacattgtctcattttctcataatggatatgatgtatctgcaaaagctgaaacaaaattgcatgcactttgtag

Basic information

species Zea mays
transcript GRMZM2G012601_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012601_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g25370.1 (Oryza sativa), 5'ss of exon 8
ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacattg----tctcattttctcataatggatatgatgtatctgcaa-aagctgaaacaaaattgcatgcactttgtag------------------------------------------
 ||||| |||||||||||||||||||||||||| || ||||||||||||||||||| ||| | |||||||||||||  | ||||    |  |  || ||   |||  ||||| | ||  || || ||| | |||   ||||  |||   ||| |                                            
GTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAGgtaccaaattggatcttgcgcttcctgccaatttatatgctctacttggaagaagttaaaatggaatt-tatgatttttttttcaagtgaaattaactggttttgaaattggttgtctttcatag
















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|13558577|gb|BG549933.1|BG549933
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG                         AAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
EST: gi|87157176|gb|DY401965.1|DY401965
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG                         AAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
EST: gi|13558246|gb|BG549602.1|BG549602
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG                         AAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
EST: gi|211396604|gb|FL446415.1|FL446415
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG                         AAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
EST: gi|211220526|gb|FL333428.1|FL333428
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG                         AAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
EST: gi|32827453|gb|CD967131.1|CD967131
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG                         AAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
EST: gi|211205847|gb|FL344232.1|FL344232
EST:     AGAGATATGGACCTCATTTTTGGACAG                         AAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
genomic: AGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
EST: gi|16380338|gb|BI993438.1|BI993438
EST:     ACTTCTACAGCAGAGATATGGACCTCATTTTTGGGCAG                         AAGCAAATACACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
genomic: ACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
EST: gi|22542734|gb|BU093172.1|BU093172
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG                         AAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
EST: gi|211414363|gb|FL328793.1|FL328793
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG                         AAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
EST: gi|211288878|gb|FL323799.1|FL323799
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG                         AAGCAAATGCACTACTTCCGCAG-AGGACGGCAAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
EST: gi|21809632|gb|BQ667950.1|BQ667950
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG                         AAGCAAATGCGCTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
EST: gi|211396603|gb|FL446414.1|FL446414
EST:     TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG                         AAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTG
EST: gi|211027850|gb|FL309697.1|FL309697
EST:     TCAAATACATTGACTTCTACAGCAGAKATATGGACCTCATTTTTGGACAG                         AAGCAAATGCACTACTKCCGCAG-AGGTACGGCAAAGGAAATACTGAGTTT
genomic: TCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGG-ACGGCAAAGGAAATACTGAGTTT

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: 68

ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTGAGGGCTGAATAAACCTTGGAGGACATCATAGGTCATTTTGGTTAGGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 20

ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTGAGGGCTGAATAAACCTTGGAGGACATCATAGGTCATTTTGGTTAGGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTGAGGGCTGAATAAACCTTGGAGGACATCATAGGTCATTTTGGTTAGGTTC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 24

ATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAGgtaatacatt ... cactttgtagAAGCAAATGCACTACTTCCGCAGGAGGACGGCAAAGGAAATACTGAGTTTGAGGGCTGAATAAACCTTGGAGGACATCATAGGTCATTTTGGTTAGGTTC