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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccataccagtctttttttaatcaaattgctgtattaggcagttcaaccattttattttacttgtgcatctttgttaattctacatgtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT

Basic information

species Zea mays
transcript GRMZM5G850355_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G850355_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 2
tgccataccagtctttttttaatcaaattgctgtattaggcagttcaaccattttatttta--cttgtgcatct-ttgttaattctacatgtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT
|    |   |||   |  | |   | | | | || |   |    ||  |  ||   |||||  || ||  ||   || | |  | ||  ||| |||||||||||||| || |||||||| || ||||| ||||||||| |||||||||||||||| ||||||||||||
ttttgtgt-agttactgctcag--agactacagtctgttgattctcttcagttcccttttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT

upper sequence: GRMZM5G850355_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 2
tgccataccagtctttttttaatcaaattgctgtattaggcagttcaaccattttatttta--cttgtgcatct-ttgttaattctacatgtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT-----------------------------------
|    |   |||   |  | |   | | | | || |   |    ||  |  ||   |||||  || ||  ||   || | |  | ||  ||| |||||||||||||| || |||||||| || ||||| ||||||||| |||||||||||||||| ||||||||||||                                   
ttttgtgt-agttactgctcag--agactacagtctgttgattctcttcagttcccttttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCTGTAAGTCTAACATCACTCTTAATGCTGAATTCCTC

upper sequence: GRMZM5G850355_T05 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 3
tgccataccagtctttttttaatcaaattgctgtat----taggcagttcaaccattttattttac-ttgtgcatct--ttgttaattctacatgtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT
        |  ||| |  ||  |    ||   || |    |||   |||  |    | || | ||  ||||   | |  || |   ||     | | || ||||||||||| || || || || |||||||||||||||||| |||| ||||| || || ||||||||||| 
-------actctctgtgcttcgttgggttctcgtgtcttgtagatggtttgaatcctgtaatgtatgttgtagttgtaattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA

upper sequence: GRMZM5G850355_T05 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 3
tgccataccagtctttttttaatcaaattgctgtattaggcagttcaaccattttattttacttgtgc-atctttgttaat---tctacatgtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT
     |||   ||| |  || ||    ||  ||| |   | || | |      |  | | |  | |||  |  ||| | ||   | |   | | ||  |||||||||| || || || || ||||| |||||||||||| |||| ||||| || || ||||||||||| 
---tttactc-tctgtggttcattgggttcttgtgtcttgtagatgatttggatcctctaatgtatgctgtagttgcttatatatttgattttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA

upper sequence: GRMZM5G850355_T05 (Zea mays), 3'ss of exon 2
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 3'ss of exon 2
----tgccataccagtctt--tttttaatcaaatt--gctgtattaggcagttcaaccattttattttacttgtgcatctttgttaattctacatgtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT
    || ||||   || ||  ||| |  |||||||  |   |||| || ||||||    | || |   | |      |   |  || || | | ||| |    |||||||||||| ||||| || ||||| || ||||||||||| |||||||| || ||||||||  |||| 
aatgtggcataatggttttgatttgttctcaaatttggtcatatttgg-agttca----tcttgtcccattaccaattgactaatacttttgcctgttac---tgcagCTGCCAATGGTGTTGTTATTGCAACTGAGAAGAAACTACCTTCTATCTTGGTGGATGAGGCATCG

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|211362042|gb|FL326986.1|FL326986
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|14203539|gb|BG837216.1|BG837216
EST:     CCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: CCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|15427202|gb|BI543024.1|BI543024
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|32934694|gb|CF039506.1|CF039506
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|22520740|gb|BU079551.1|BU079551
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGGGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|5566889|gb|AI881800.1|AI881800
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGGGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|87156656|gb|DY401445.1|DY401445
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGGGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211218837|gb|FL350383.1|FL350383
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|14242859|gb|BG840665.2|BG840665
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|32908069|gb|CF012882.1|CF012882
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211411607|gb|FL320443.1|FL320443
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211372616|gb|FL325639.1|FL325639
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211408164|gb|FL390201.1|FL390201
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|71331110|gb|DR802381.1|DR802381
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|9461620|gb|BE453822.1|BE453822
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211156517|gb|FL164231.1|FL164231
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|14204267|gb|BG837944.1|BG837944
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|29167732|gb|CB410992.1|CB410992
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211100498|gb|FL307608.1|FL307608
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|28931244|gb|CB334605.1|CB334605
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211028588|gb|FL333340.1|FL333340
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211040642|gb|FL333768.1|FL333768
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|8367928|gb|BE050873.1|BE050873
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAATGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|31910204|gb|CD651307.1|CD651307
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|12967998|gb|BG264945.1|BG264945
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|5456381|gb|AI834071.1|AI834071
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGGGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211158124|gb|FL164253.1|FL164253
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|40337252|gb|CK371322.1|CK371322
EST:     GGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211227292|gb|FL365228.1|FL365228
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|26559204|gb|CA831439.1|CA831439
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGGGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211352174|gb|FL343457.1|FL343457
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|5456374|gb|AI834064.1|AI834064
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGGGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|211401638|gb|FL329192.1|FL329192
EST:     GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|31355634|gb|CD439991.1|CD439991
EST:     GGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAATGGTGTATTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
genomic: GGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG
EST: gi|32906923|gb|CF011736.1|CF011736
EST:     GCACGCGCTCACTGTTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAG                         CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGG
genomic: GCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAG

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: 727

CCCGTCGGGAAAGCTTGTGCAGATAGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 668

CCCGTCGGGAAAGCTTGTGCAGATAGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 452

CCCGTCGGGAAAGCTTGTGCAGATAGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 533

CCCGTCGGGAAAGCTTGTGCAGATAGAGCACGCGCTCACGGCTGTCGGATCCGGGCAGACCTCCCTAGGGATCAAAGgttcgatctg ... atgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaccattttattttacttgtgcatctttgttaattctacatgtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT
                            tgttaat  putative branch site (score: 533)
     attttattttacttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccataccagtctttttttaatcaaattgctgtattaggcagttcaaccattttattttacttgtgcatctttgttaattctacatgtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA