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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaactcaatgcccttcgtatgctacaggatgctttatttttttatacatctgttttactattgcaatgccatttaactttgctgatattcttttcaggagTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCCTTGTTTCTCACCATATTCCTTATTCTTGCACCAGTGGTGGTCTTCTGCATATTTG

Basic information

species Zea mays
transcript GRMZM2G179002_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179002_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g33450.2 (Oryza sativa), 3'ss of exon 2
aaactcaatgcccttcgtatg---ctacaggatgctttatttttttatacatctgttttac-tattgcaatgccatttaact-ttgctgatattcttttcaggagTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCCTTGTTTCTCACCATATTCCTTATTCTTGCACCAGTGGTGGTCTTCTGCATATTTG
   || |  |   ||  |||      ||       |||    || | |      |||| ||  |||| | |      ||||  ||   ||| || ||||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||||||||| |||||||| ||||||||||||||  | |||||||| ||||   
--gctgaccgttttttttataaattcacttatatatttgcaattatttcttctagtttcacgcattggattcattgataacaattatggatctttttttcagGAGTTTTTCTTGCAAGGCCGGTTCATTTTTGGACCAGATGTGAGATCTTTGTTTCTCACTATATTCCTCATTCTTGCACCAGTATTAGTCTTCTGTATAT---
















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|211247328|gb|FL045401.1|FL045401
EST:     CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCGA-GGAAGCAAC                         G
genomic: CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGC-ATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|211247328|gb|FL045401.1|FL045401
EST:     CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCGA-GGAAGCAAC                         G
genomic: CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGC-ATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|211247328|gb|FL045401.1|FL045401
EST:     CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCGA-GGAAGCAAC                         G
genomic: CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGC-ATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|211247328|gb|FL045401.1|FL045401
EST:     CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCGA-GGAAGCAAC                         G
genomic: CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGC-ATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|91054809|gb|EB165227.1|EB165227
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|91054809|gb|EB165227.1|EB165227
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|91054809|gb|EB165227.1|EB165227
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|91054809|gb|EB165227.1|EB165227
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|149111808|gb|EE190960.2|EE190960
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|149111808|gb|EE190960.2|EE190960
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|149111808|gb|EE190960.2|EE190960
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|149111808|gb|EE190960.2|EE190960
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|211245109|gb|FL045400.1|FL045400
EST:     CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCGA-GGAAGCAAC                         G
genomic: CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGC-ATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|211245109|gb|FL045400.1|FL045400
EST:     CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCGA-GGAAGCAAC                         G
genomic: CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGC-ATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|211245109|gb|FL045400.1|FL045400
EST:     CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCGA-GGAAGCAAC                         G
genomic: CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGC-ATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|211245109|gb|FL045400.1|FL045400
EST:     CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCGA-GGAAGCAAC                         G
genomic: CGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGC-ATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|149009674|gb|EE041607.2|EE041607
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|149009674|gb|EE041607.2|EE041607
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|149009674|gb|EE041607.2|EE041607
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|149009674|gb|EE041607.2|EE041607
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|148936630|gb|EC880754.2|EC880754
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         TTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCCTTGTTT
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggagTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCCTTGTTT
EST: gi|148992698|gb|EE033657.2|EE033657
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|148992698|gb|EE033657.2|EE033657
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|148992698|gb|EE033657.2|EE033657
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|148992698|gb|EE033657.2|EE033657
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|148947125|gb|EC892437.2|EC892437
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|148947125|gb|EC892437.2|EC892437
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|148947125|gb|EC892437.2|EC892437
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-
EST: gi|148947125|gb|EC892437.2|EC892437
EST:     GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAAC                         G
genomic: GCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggag-

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: 76

GAGGGAGCTGGAGATGTACGGGCCGCCGTCCCGAGGCGGCGGGGGAGCCGGCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggagTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCCTTGTTTCTCACCATATTCCTTATTCTTGCACCAGTGGTGGTCTTCTGCATATTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 73

GAGGGAGCTGGAGATGTACGGGCCGCCGTCCCGAGGCGGCGGGGGAGCCGGCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggagTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCCTTGTTTCTCACCATATTCCTTATTCTTGCACCAGTGGTGGTCTTCTGCATATTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

GAGGGAGCTGGAGATGTACGGGCCGCCGTCCCGAGGCGGCGGGGGAGCCGGCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggagTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCCTTGTTTCTCACCATATTCCTTATTCTTGCACCAGTGGTGGTCTTCTGCATATTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

GAGGGAGCTGGAGATGTACGGGCCGCCGTCCCGAGGCGGCGGGGGAGCCGGCGCTGCCGGAGAGCAGCCGAGGGTTTACCAAGTTTGGCATGGAAGCAACgtgagccctc ... ttttcaggagTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCCTTGTTTCTCACCATATTCCTTATTCTTGCACCAGTGGTGGTCTTCTGCATATTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatctgttttactattgcaatgccatttaactttgctgatattcttttcaggagTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCCTTGTTTCTCACCATATTCCTTATTCTTGCACCAGTGGTGGTCTTCTGCATATTTG
                                  tgctgat  putative branch site (score: 103)
                                        tattcttttc  CT-rich tract
       ttttactatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaactcaatgcccttcgtatgctacaggatgctttatttttttatacatctgttttactattgcaatgccatttaactttgctgatattcttttcaggagTTTTTCTTGCAAGGCCGGTTCATATTTGGACCTGATGTGAGATCCTTGTTTCTCACCATATTCCTTATTCTTGCACCAGTGGTGGTCTTCTGCATATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
-aactcaa
- - - - tgccctt
- - - - - - - - - - gctacag
- - - - - - - - - - - - - -gatgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat