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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacactgcatattcgtttttttttcactttaaatactaacgtgtgctcctgcaccgttcgagaaaaagaaatactaatgtgtgttaataggatcccaactattcaaccatataatgttttgccatagcacataacagtgctggcacatttcttgtaaccaatttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAACATGAGGCCGGGGGATATATTTGCGACTGGCACACTGAGTGGACCT

Basic information

species Zea mays
transcript GRMZM2G029566_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029566_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g10310.1 (Oryza sativa), 3'ss of exon 11
gtaagcacactgcatattcgtttttttttcactttaaatactaacgtgtgctcctgcaccgttcgagaaaaagaaatactaatgtgtgttaataggatcccaactattcaaccatataatgttttgccata-gcacataacagtgctggcacatttcttgtaaccaatttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAACATGAGGCCGGGGGATATATTTGCGACTGGCACACTGAGTGGACCT
                                                                                       || |  | | | ||   | | | |        |   || ||||| | |  |   ||   || |    ||  |||||| | ||||| | ||||||||||||  | |||||||| ||||||||||||||  | || ||||||||  |||| || |||||||| ||||| ||||||||||| || ||||||
---------------------------------------------------------------------------------------gtaaggatgcttcctgttttccgattgc-cgtttcattaccatatgtatttgttagctttgtc---cttactgtaactattttttcc-cagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT
















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|211273148|gb|FL031471.1|FL031471
EST:     CACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: CACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|76920585|gb|DV168249.1|DV168249
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|149099313|gb|EE185349.2|EE185349
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|211273139|gb|FL031462.1|FL031462
EST:     CACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: CACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|31355627|gb|CD439984.1|CD439984
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|6403389|gb|AW171864.1|AW171864
EST:     CAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: CAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|32851376|gb|CD991057.1|CD991057
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGNAGCTAGCACACCACACCATCAACGGAT
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGAT
EST: gi|148929744|gb|EC876669.2|EC876669
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACCCCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|29545139|gb|CB605317.1|CB605317
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|211248919|gb|FL466732.1|FL466732
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCCATCAACGGATGCA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACA-CCATCAACGGATGCA
EST: gi|71328227|gb|DR800747.1|DR800747
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|148983239|gb|EE029205.2|EE029205
EST:     GCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: GCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|78124352|gb|DV542736.1|DV542736
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|60346412|gb|DN213385.1|DN213385
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|211273144|gb|FL031467.1|FL031467
EST:     CACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: CACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|83278342|gb|DV942350.1|DV942350
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|4730752|gb|AI649918.1|AI649918
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|211273143|gb|FL031466.1|FL031466
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|211059340|gb|FL474462.1|FL474462
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|211273142|gb|FL031465.1|FL031465
EST:     CAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: CAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|91052882|gb|EB163300.1|EB163300
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|211273145|gb|FL031468.1|FL031468
EST:     CACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: CACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|211273141|gb|FL031464.1|FL031464
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|149042086|gb|EE047064.2|EE047064
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACCCCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|211273140|gb|FL031463.1|FL031463
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|148946153|gb|EC891447.2|EC891447
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|86465953|gb|DY232326.1|DY232326
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|211228559|gb|FL433551.1|FL433551
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA
EST: gi|149076832|gb|EE165487.2|EE165487
EST:     AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCT                         GTATTGGACGCTGACACAGCAGCTAGCACCCCACCCCATCAACGGATGCAA
genomic: AAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAA

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: 46 (upstream exon), 48 (downstream exon)
Score: 166

GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAACATGAGGCCGGGGGATATATTTGCGACTGGCACACTGAGTGGACCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 238

GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAACATGAGGCCGGGGGATATATTTGCGACTGGCACACTGAGTGGACCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 189

GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAACATGAGGCCGGGGGATATATTTGCGACTGGCACACTGAGTGGACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1029

GCCTGGATTAAGCCGAAAGATCAAAATGACGCATCAATTGTCACAAAAACTAATTTCAAGCATCTgtaagcacac ... ttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAACATGAGGCCGGGGGATATATTTGCGACTGGCACACTGAGTGGACCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgccatagcacataacagtgctggcacatttcttgtaaccaatttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAACATGAGGCCGGGGGATATATTTGCGACTGGCACACTGAGTGGACCT
                                  ttgtaac  putative branch site (score: 1029)
                                            tttttgc  putative PPT
                                          aattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacactgcatattcgtttttttttcactttaaatactaacgtgtgctcctgcaccgttcgagaaaaagaaatactaatgtgtgttaataggatcccaactattcaaccatataatgttttgccatagcacataacagtgctggcacatttcttgtaaccaatttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAACATGAGGCCGGGGGATATATTTGCGACTGGCACACTGAGTGGACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA