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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcgttactcttcatttttcaattaaagttatacatgaacacttccataatcccctctgctacattttatctatgtaataagtaatttattgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTG

Basic information

species Zea mays
transcript GRMZM2G149704_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149704_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 2
gttagcgttactcttcatttttcaattaaagttatacatgaacacttccataatcccctctgctacattttatctatgtaataagtaatttatt-gtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTG
        || | |  |||||   |||| |  ||  ||        ||| |  ||  || |||||   || || ||  |  |   |   |  ||   || |||| |||| ||||| |||||||| |||||  ||||||||||||||||||| ||| | ||| | || |   | |||| | | ||||||||| |   | |  | 
---catactattttatattttgacattagatgtactcaattctttatccttgttcaactgtgctatgcttgatttaatttttgctttgctgcttcaattgcagTACTGCTTGCATGAAGCTTGAGGAATATGAAACTGCAAAGGCTGCTCTGGAGGTGGGTGCATCATTGTCTCCAGACAACTCAAGGTTTGCTACTTTGATC
















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|211045632|gb|FL292671.1|FL292671
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTAATCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
EST: gi|78080588|gb|DV509000.1|DV509000
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
EST: gi|211045637|gb|FL292676.1|FL292676
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTAATCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
EST: gi|89757539|gb|DY687098.1|DY687098
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
EST: gi|149076474|gb|EE165099.2|EE165099
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
EST: gi|32801805|gb|CD954041.1|CD954041
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGTATTA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTA
EST: gi|211042677|gb|FL292666.1|FL292666
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
EST: gi|32791338|gb|CD943574.1|CD943574
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTA
EST: gi|29947233|gb|CB816549.1|CB816549
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
EST: gi|149104781|gb|EE290244.2|EE290244
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
EST: gi|211045636|gb|FL292675.1|FL292675
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
EST: gi|211045634|gb|FL292673.1|FL292673
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTAATCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
EST: gi|148975634|gb|EE025764.2|EE025764
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
EST: gi|211045630|gb|FL292669.1|FL292669
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTAATCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
EST: gi|31612314|gb|CD568936.1|CD568936
EST:     AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGG                         TGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA
genomic: AAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGA

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: 297

AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 310

AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 341

AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

AGGCTGTGGCAGATGCTAACAAAGCAATTGGTCTTGATCCTACAATGCATAAAGCCTACTACCGGAAAGGgttagcgtta ... ttgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccataatcccctctgctacattttatctatgtaataagtaatttattgtttacagTGCTGCATGCATTAAGCTTGAAGAATACCAAACTGCAAAGGCTGCTCTTGAGTTAGGTTCTTCCTATGCACCAGGCGATTCAAGGTTTACCCGTCTATTG
                tacattttatctatgt  TA-rich tract