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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcataaattgaatttaagaactgaaacttgctattttgtaccattccagaaagagcgttataatttcccactttacctgacatttgttccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGCCTGTTATTATGCCTAATTCGCTAGGCATGGCATTTCCTCCGCGACCAGC

Basic information

species Zea mays
transcript GRMZM2G081812_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081812_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 2
atgcataaattgaatttaagaactgaaacttgctattt-tgtaccattccagaaagagcgttataa----tttcccactttacctgacatttgttccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGCCTGTTATTATGCCTAATTCGCTAGGCATGGCATTTCCTCCGCGACCAGC
     | | |    | || ||| | ||  || |  |   | || |   ||| | |      |||||    ||    ||||||  |      ||||| |  ||||||||||||||||||| | |||||| ||||||| ||||||||   | ||||||||  | ||||||| ||| |    ||||||| || |||||| ||||| ||
-----ttattcatgtgtaggaattaaatattccagtgagtttaaccagccatatattttcctataagaacttgttaactttatttagttcatgttctaaatgcagAGGAAGACCCTTCATCGAAGGTAGCCAAAGTGGAAGTGCCATCGCTAAGGCCTCCTGTTATGCCCAATCCAGCGGGCATGGTATATCCTCCACGACCGGC
















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|211062251|gb|FL249756.1|FL249756
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAAGTAGAAGTGCCTCAGGTAAGG
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCC-AAAGTAGAAGTGCCTCAGGTAAGG
EST: gi|31361671|gb|CD446028.1|CD446028
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|71325031|gb|DR799198.1|DR799198
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|24462593|gb|BM660124.1|BM660124
EST:     ATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: ATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|74034907|gb|DT535397.1|DT535397
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGTCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|26457010|gb|CA828593.1|CA828593
EST:     TGGAATGCAGGGAATTCCTTCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|211108805|gb|FL115292.1|FL115292
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|22818963|gb|BU499053.1|BU499053
EST:     TGGAATGCAGGGAATTCCTTCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|211109705|gb|FL115302.1|FL115302
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|87155380|gb|DY400169.1|DY400169
EST:     TGGAATGCAGGGAATTCCTTCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|26457257|gb|CA828840.1|CA828840
EST:     TGGAATGCAGGGAATTCCTTCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|29946767|gb|CB816315.1|CB816315
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGGCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|32910104|gb|CF014916.1|CF014916
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|211108807|gb|FL115294.1|FL115294
EST:     TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCA
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCA
EST: gi|26559878|gb|CA832113.1|CA832113
EST:     TGGAATGCAGGGAATTCCTTCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC
EST: gi|22543269|gb|BU093707.1|BU093707
EST:     TGGAATGCAGGGAATTCCTTCGCATGTATTGGCTGCTCATTATGGAGAAG                         AGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAG-GCCTCAGGTAAGGC
genomic: TGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGC

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: 47 (upstream exon), 47 (downstream exon)
Score: 420

GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGCCTGTTATTATGCCTAATTCGCTAGGCATGGCATTTCCTCCGCGACCAGC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 253

GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGCCTGTTATTATGCCTAATTCGCTAGGCATGGCATTTCCTCCGCGACCAGC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 323

GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGCCTGTTATTATGCCTAATTCGCTAGGCATGGCATTTCCTCCGCGACCAGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 258

GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGGAATGCAGGGAATTCCTGCGCATGTATTGGCTGCTCATTATGGAGAAGgtatgcagat ... ccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGCCTGTTATTATGCCTAATTCGCTAGGCATGGCATTTCCTCCGCGACCAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccagaaagagcgttataatttcccactttacctgacatttgttccacgtgcagAGGAAGACCCTTCAACAAAGGTACCCAAAGTAGAAGTGCCTCAGGTAAGGCCTGTTATTATGCCTAATTCGCTAGGCATGGCATTTCCTCCGCGACCAGC
                               acctgac  putative branch site (score: 258)
                                       tttgttcc  CT-rich tract
              ttataattt  TA-rich tract