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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTTACATCTCCAGGTTATGGTGAACTCTACAGAGAAAGTAAGGCTTGCTGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcatcttttggttctttattttctgtttgttgcccacttaaacatgaaaaagatacaacaattaatcataggaactaaggaaagtaggtaacat...

Basic information

species Zea mays
transcript GRMZM2G168510_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168510_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os12g10784.1 (Oryza sativa), 5'ss of exon 7
CATTTACATCTCCAGGTTATGGTGAACTCTACAGAGAAAGTAAGGCTTGCTGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat-------cttttggttctttattttctgtttgttgcccacttaaacatgaaaaagatacaacaattaatcataggaactaaggaaagtaggtaacat
               |||||||  |||||| |||||||| | || |||||||| |||| |||||| ||||||||||||||||| ||||||||||||||||||||||| ||       ||||||| | | |  |||||||   |||| || || || || | | | |   || | | |   ||   ||   | || | | | |     
---------------GTTATGGCCAACTCTGCAGAGAAAATCAGACTTGCTGGAAATCAAAATGTTATGGTCTGTGAGCGTGGCACCATGTTTGGCTACAgttaaggaatatatattcttttggctatct--tttctgtacattgctcaatttaagataacacaaagtgaaaagtcatagatgtaaatatatgatattggat-----

upper sequence: GRMZM2G168510_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT1G16340.2 (Arabidopsis thaliana), 5'ss of exon 8
CATTTACATCTCCAGGTTATGGTGAACTCTACAGAGAAAGTAAGGCTTGCTGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgtta---aggcatcttttggttcttta---ttttctgtttgttgcccacttaaacatgaaaaagatacaacaattaatcataggaactaaggaaagtaggtaacat------------------
               || |||   |||||  | ||||| || || || || |||||||||||||||||||| |||||  | || ||||||||||| |||||| |   |    |  ||||  ||  ||   ||  |   || ||   ||  || | |  ||||      || |   | |      ||||   ||  ||   || |||                  
---------------GTCATGAGAAACTCGGCTGAGAAGGTTAGACTCGCAGGGAATCCAAATGTGATGGTTTGTGAAAGAGGAACCATGTTTGGATACAgtaagttaactgttctttgtgtcaatagaattcaccaatttttttgcaaatagagactaaaatagactaaaagacactggatataactcctgagtgtcctta-cattttaattttgttcctcag

upper sequence: GRMZM2G168510_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ32189 (Selaginella moellendorffii), 5'ss of exon 6
CATTTACATCTCCAGGTTATGGTGAACTCTACAGAGAAAGTAAGGCTTGCTGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcatcttttggttctttattttctgtttgttgcccacttaaacatgaaaaagatacaacaattaatcataggaactaaggaaagtaggtaacat
               || |||   || ||  | |  ||  | ||||||||||| |||||||| || |||||||||||||| || ||||||||||||||||||  | | || |||||| |    | ||      || ||     |    |  ||      |  |                                     
---------------GTGATGACCAATTCAGCCGCTAAGATCAGGCTTGCTGGAAATCCAAACGTCATGGTCTGTGAGCGCGGCACCATGTTTGGCTACAgt--aagtattttttggattccaaattct--cctgctgagtggtgtggctggattttcgtgtag------------------------------------

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|31362214|gb|CD446571.1|CD446571
EST:     TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACA                         ATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
genomic: TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
EST: gi|60359317|gb|DN226290.1|DN226290
EST:     TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACA                         ATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
genomic: TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
EST: gi|60340487|gb|DN207460.1|DN207460
EST:     CGTGGTTACCATGTTTGGCTACA                         ATGATCTATTTG-TGACCCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAAC
genomic: CGTGG-TACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGA-CCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAAC
EST: gi|5871261|gb|AW017732.1|AW017732
EST:     TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACA                         ATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
genomic: TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
EST: gi|60400102|gb|DN232909.1|DN232909
EST:     CAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACA                         ATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
genomic: CAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
EST: gi|74236360|gb|DT644274.1|DT644274
EST:     TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACA                         ATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
genomic: TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
EST: gi|60398159|gb|DN230975.1|DN230975
EST:     TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACA                         ATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
genomic: TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
EST: gi|71763878|gb|DR961815.1|DR961815
EST:     TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACA                         ATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
genomic: TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
EST: gi|26558981|gb|CA831216.1|CA831216
EST:     TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACA                         ATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
genomic: TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
EST: gi|211051797|gb|FL187615.1|FL187615
EST:     TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACA                         ATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
genomic: TGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
EST: gi|33101621|gb|CF061581.1|CF061581
EST:     GGTACCATGTTTGGCTACA                         ATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
genomic: GGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
EST: gi|4730747|gb|AI649913.1|AI649913
EST:     ACCATGTTTGGCTACA                         ATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT
genomic: ACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACT

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: 48 (upstream exon), 49 (downstream exon)
Score: 125

CATTTACATCTCCAGGTTATGGTGAACTCTACAGAGAAAGTAAGGCTTGCTGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACTGCCCAGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91

CATTTACATCTCCAGGTTATGGTGAACTCTACAGAGAAAGTAAGGCTTGCTGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACTGCCCAGTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 103

CATTTACATCTCCAGGTTATGGTGAACTCTACAGAGAAAGTAAGGCTTGCTGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACTGCCCAGTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 75

CATTTACATCTCCAGGTTATGGTGAACTCTACAGAGAAAGTAAGGCTTGCTGGGAATCCAAATGTGATGGTCTGTGAGCGTGGTACCATGTTTGGCTACAgttaaggcat ... taacacacagATGATCTATTTGTTGACCCAAGGAACCTTGAGTGGCTGAGGGAAAGCAACTGCCCAGTT