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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgtccacatcatttctgtgatcaatgtataactaaatattcctactgttaaatttgtttcctttatgaaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGCATCATAGTGTCCAGTTCTATGTGTCAGCGCCGGTAACTTCCATTGATCT

Basic information

species Zea mays
transcript GRMZM2G139533_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139533_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g11050.1 (Oryza sativa), 3'ss of exon 8
--gtaaatgtccacatcatttctgtgatcaatgtataactaaatattcctactgttaaatttgtttcctttatgaaatttc-aagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGCATCATAGTGTCCAGTTCTATGTGTCAGCGCCGGTAACTTCCATTGATCT
    | |  || |  ||||| ||  ||| |||  | ||||||| |||| | || || | ||||||||| | || |||| || ||||||| || || ||||||||||||||||||||||||||||| || |||||||||||  |||| || ||||| ||| | |||||| ||||||| ||||||||
gtacacacatcaatgtcattcctcagatgaattgaaaactaaaaattcttgctattgactttgtttccatcataaaatctccaagGTGATACTGCTAACAAGATTGGCACATACAACCTCGCCATTTCTGCGAAGCATCACGGTGTGCAATTCTACGTGGCTGCGCCGATAACTTCGATTGATCT
















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|76285910|gb|DV025478.1|DV025478
EST:     GGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: GGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|76017068|gb|DT944238.1|DT944238
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|60359093|gb|DN226066.1|DN226066
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATATAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|78116800|gb|DV535187.1|DV535187
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATA
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATA
EST: gi|37398320|gb|CF636472.1|CF636472
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|71445094|gb|DR826144.1|DR826144
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|211030875|gb|FL442918.1|FL442918
EST:     GGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAACAAAAG                         GTAACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|60352019|gb|DN218992.1|DN218992
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|211279443|gb|FK979043.1|FK979043
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|78180539|gb|DV551032.1|DV551032
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|67021902|gb|CO450651.1|CO450651
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATATAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|211506055|gb|FL476284.1|FL476284
EST:     GCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: GCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|88749182|gb|DY533323.1|DY533323
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|6964770|gb|AW433463.1|AW433463
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|88756069|gb|DY540210.1|DY540210
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|211470410|gb|FL454226.1|FL454226
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATATAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|71756819|gb|DR954756.1|DR954756
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
EST: gi|74233419|gb|DT641333.1|DT641333
EST:     AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATG                         GTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC
genomic: AGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGC

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: 212

ATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGCATCATAGTGTCCAGTTCTATGTGTCAGCGCCGGTAACTTCCATTGATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

ATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGCATCATAGTGTCCAGTTCTATGTGTCAGCGCCGGTAACTTCCATTGATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

ATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGCATCATAGTGTCCAGTTCTATGTGTCAGCGCCGGTAACTTCCATTGATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

ATACCTGCAACACTGATAGCAGATTCTGCTGCTGCTGCGTTGATGAAACAAGGGCATGTTCAGGCTGTCATTGTTGGTGCTGATCGAATAGCAGCAAATGgtaaatgtcc ... aaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGCATCATAGTGTCCAGTTCTATGTGTCAGCGCCGGTAACTTCCATTGATCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtataactaaatattcctactgttaaatttgtttcctttatgaaatttcaagGTGACACAGCCAACAAGATTGGCACATACAACCTCGCCATCTCCGCGAAGCATCATAGTGTCCAGTTCTATGTGTCAGCGCCGGTAACTTCCATTGATCT
       aactaaa  putative branch site (score: 201)
                                       tttatgaaatttcaa  TA-rich tract