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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaacccactaaccttttagataaacatatagacactaactgtattccgtttgatggttattgcttctgttttacctcattggccattttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCAATGGCTCACGTACTGGGTGCTGTACTCATTTATCACTCTATTCGAGCTC

Basic information

species Zea mays
transcript GRMZM2G130548_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130548_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g51290.2 (Oryza sativa), 3'ss of exon 2
gtaagttaacccactaaccttttagataaacatatagacactaactgtattccgtttgatggttattgcttctgttttacctcattggccattttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCAATGGCTCACGTACTGGGTGCTGTACTCATTTATCACTCTATTCGAGCTC
||||||||  |||  |   | ||   ||   | ||| | ||  ||| | || | ||   | |||                || ||||| ||  ||  |||| ||||| |||||| |||| || ||||||||||||||||| |||||||||||||||||||| ||||||||| ||||||| |||||||||||||| ||||||
gtaagttactccagcactttcttttgtatgta-ataaatacatact-tcttgcattc--tagtt----------------ctgattggacaccttt-acagATATGCATCTGTTCGAGCGATAGAAACAAAATCTGCTGTAGATGATCAGCAATGGCTCACATACTGGGTGTTGTACTCGTTTATCACTCTATTTGAGCTC

upper sequence: GRMZM2G130548_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G33880.1 (Glycine max), 3'ss of exon 2
--------gtaagttaacccactaaccttttagataaacatatagacactaactgtattccgtttgatggttattgcttctgttttacctcattggccattttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCAATGGCTCACGTACTGGGTGCTGTACTCATTTATCACTCTATTCGAGCTC
         | | ||  |    |    || |   | ||  ||| |      | || ||   | |||||  | || | || || |||   | | |     ||     ||| |||||||| ||||| |||||||| |  || ||| |||| ||||| |||||||||||||| || ||||| || ||||| || ||||| || || || || 
tgtttgtttttattttgctggttcttgttatgtgttaagctattgttggagaatgaata--gattgat--tcatggtttgtgatttctttgaataatgctt-----cagATATGCCTCGGTTAGGGCAATTGAGAGCAAGTCTCCTGTTGATGACCAGCAATGGCTCACTTATTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT

upper sequence: GRMZM2G130548_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
gtaagttaacccactaaccttttagataaacatatagacactaactgtattccgtttgatgg-ttattgcttctgttttacctcattggccattttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCAATGGCTCACGTACTGGGTGCTGTACTCATTTATCACTCTATTCGAGCTC
  | ||     |  |||  | |    | ||  | |      ||  | | |        || | ||    ||| ||||||       |||   | ||  |||| ||||||||  |||| |||||||| || || ||  |||| |||||||||||||||||||| ||||||||  |||| ||  | ||||| || |||||||||
-catgtatgttctataatatgtggtttgaatgtttgtgttttagttttctgagagaaaattgcttgaaacttttgttttggtgggctggtt-tctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC

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|211070403|gb|FL012978.1|FL012978
EST:     GCCTTTGGTTTCACTTGCGTATCCTCT                         GTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
genomic: GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
EST: gi|89755506|gb|DY685902.1|DY685902
EST:     GCCTTTGGTTTCACTTGCGTATCCTCT                         GTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
genomic: GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
EST: gi|211067663|gb|FL012963.1|FL012963
EST:     GCCTTTGGTTTCACTTGCGTATCCTCT                         GTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
genomic: GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
EST: gi|211070406|gb|FL012981.1|FL012981
EST:     GCCTTTGGTTTCACTTGCGTATCCTCT                         GTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
genomic: GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
EST: gi|211064940|gb|FL012961.1|FL012961
EST:     GCCTTTGGTTTCACTTGCGTATCCTCT                         GTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
genomic: GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
EST: gi|211070408|gb|FL012983.1|FL012983
EST:     GCCTTTGGTTTCACTTGCGTATCCTCT                         GTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
genomic: GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
EST: gi|211067666|gb|FL012966.1|FL012966
EST:     GCCTTTGGTTTCACTTGCGTATCCTCT                         GTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
genomic: GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
EST: gi|211070404|gb|FL012979.1|FL012979
EST:     GCCTTTGGTTTCACTTGCGTATCCTCT                         GTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
genomic: GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
EST: gi|211067676|gb|FL012976.1|FL012976
EST:     GCCTTTGGTTTCACTTGCGTATCCTCT                         GTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
genomic: GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
EST: gi|211067664|gb|FL012964.1|FL012964
EST:     GCCTTTGGTTTCACTTGCGTATCCTCT                         GTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA
genomic: GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCA

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: 27 (upstream exon), 49 (downstream exon)
Score: 479

GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCAATGGCTCACGTACTGGGTGCTGTACTCATTTATCACTCTATTCGAGCTC


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 225

GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCAATGGCTCACGTACTGGGTGCTGTACTCATTTATCACTCTATTCGAGCTC


Block sizes: 27 (upstream exon), 48 (downstream exon)
Score: 142

GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCAATGGCTCACGTACTGGGTGCTGTACTCATTTATCACTCTATTCGAGCTC


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 271

GCCTTTGGTTTCACTTGCGTATCCTCTgtaagttaac ... ttttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCAATGGCTCACGTACTGGGTGCTGTACTCATTTATCACTCTATTCGAGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattccgtttgatggttattgcttctgttttacctcattggccattttccacagGTATGCCTCTGTTAGAGCAATTGAAACAAAATCTGCTGTGGATGATCAGCAATGGCTCACGTACTGGGTGCTGTACTCATTTATCACTCTATTCGAGCTC
       gtttgat  putative branch site (score: 271)
                                          ccattttcc  putative PPT
                          tgtttta  TA-rich tract