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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGCAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaatggactctgatgtttcttaatctagttacctataaccatatagatgttcttgctattgtgaaaatagtgttttcacataacacacggtgagcttaatgttgggcag

Basic information

species Zea mays
transcript GRMZM2G083344_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083344_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g15160.1 (Oryza sativa), 5'ss of exon 10
GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGCAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaatggactctgatgtttcttaat--ctagttacctataaccatatagatgttcttgctattgtgaaa----atagtgttttcacataacacacggtgagcttaatgttgggcag---------------------------------------------------
||||||||||||||||| ||  ||||  ||||| ||||||||||  | ||||||||||| |||||||| |||||||||||||| || ||||| |||||||||||||   |  | | | || |||| ||||   |    | |  ||  |||||   ||||||||| ||||  ||      || | ||||    ||  ||    |   | || | || |   |                                                   
GTTGCTACAAACACATTAGAAAGGGTGACCCCTCTAACACATGCTGTTGGCAATGTGTTAAAACGTGTCTTCGTCATTGGCTTCTCAATCATTGCATTCGgtactt---ttaattttaatctttcataatgattgtcgatcagtatgcatattcttgttcttgccattggcaagtgttgtactctttttttgtagaacttcatatacatagttttagtgtgcaaatgatctgatgtttttgtgtaatacttggtgaacttaatgttgaacag
















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|8665718|gb|BE186534.1|BE186534
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|211430251|gb|FL453372.1|FL453372
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGNAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|211525667|gb|FL445646.1|FL445646
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|71760100|gb|DR958037.1|DR958037
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|32928246|gb|CF033058.1|CF033058
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|5018389|gb|AI714582.1|AI714582
EST:     TCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGGTCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: TCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|32165070|gb|CD670388.1|CD670388
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|37381423|gb|CF627595.1|CF627595
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|71328475|gb|DR800887.1|DR800887
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|76930049|gb|DV172255.1|DV172255
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|71768355|gb|DR966292.1|DR966292
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|32935156|gb|CF039968.1|CF039968
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|32862760|gb|CF002442.1|CF002442
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|211083989|gb|FL462610.1|FL462610
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|113703585|gb|EE681089.1|EE681089
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|50328059|gb|CO523185.1|CO523185
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|78104082|gb|DV522500.1|DV522500
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTGG                         GCAACAAGATCCCCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
EST: gi|32837170|gb|CD976848.1|CD976848
EST:     CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCG                         GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG
genomic: CAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTG

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), 47 (downstream exon)
Score: 185

GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGCAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 17

GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGCAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 30

GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGCAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 50

GTTGCTACAAACACATTGGAGCGGGTAGCCCCTTTAACACATGCCATCGGCAATGTGTTGAAACGTGTTTTCGTCATTGGCTTTTCCATCATCGCATTCGgtacttgaat ... tgttgggcagGCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG