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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acctctttcatcatagtagtagttgcatattacaattgtgactcaccaagtcaccattgctgtcattcccgtactgattccatatcattttgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGAAGTGATCTCCAGCTTATTTCCAACACATATTTATTAAGTCATCTTTGAC

Basic information

species Zea mays
transcript GRMZM2G165535_T05
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165535_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g58580.1 (Oryza sativa), 3'ss of exon 10
----acctctttcatcatagtagtagttgcatattacaattgtgactcaccaagtcaccattgctgtcattcccgtactgattccatatcattttgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGAAGTGATCTCCAGCTTATTTCCAACACATATTTATTAAGTCATCTTTGAC
      ||  ||   |   ||   | |||| |  || |  | |      | ||  ||  |||| || |||  ||   |||||| |||  |||||  ||||||||||||||| ||   ||| |||||  |||| ||||||||||||||  ||||||||||| ||        |       |  |||||   |   |||   | ||
ctgagtcttgtttgccgaggttaaacttgctt--taaatcttttctgagctaatacatgattgatgccatcaccaagctgatttcat--catttatatttgcagTTACCAGTCCTGATGATACAGCAGAGCAGTGCAGATCTCTCTTCATGTCGAAGTGACCTGATTACCGTGCATTTTATTTATTTTACATAGCATTCCTCAC
















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|6020771|gb|AW065579.1|AW065579
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|5871671|gb|AW018142.1|AW018142
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|78118501|gb|DV536885.1|DV536885
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|86471496|gb|DY237866.1|DY237866
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|85151824|gb|DW587525.1|DW587525
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATCCAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|40334667|gb|CK368737.1|CK368737
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|76011520|gb|DT938690.1|DT938690
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|5361143|gb|AI795758.1|AI795758
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|211038831|gb|FL468651.1|FL468651
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|71763428|gb|DR961365.1|DR961365
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|45846830|gb|CN070773.1|CN070773
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|32919709|gb|CF024521.1|CF024521
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|14700950|gb|BI233368.1|BI233368
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|148947648|gb|EC893128.2|EC893128
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|148943662|gb|EC888726.2|EC888726
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|5871104|gb|AW017545.1|AW017545
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|148947872|gb|EC893365.2|EC893365
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|40302745|gb|CK347132.1|CK347132
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|71299718|gb|DR785869.1|DR785869
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|32909183|gb|CF013995.1|CF013995
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|76280414|gb|DV019982.1|DV019982
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
EST: gi|32909184|gb|CF013996.1|CF013996
EST:     TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAG                         TTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA
genomic: TGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGA

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: 40 (upstream exon), 49 (downstream exon)
Score: 11

GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGAAGTGATCTCCAGCTTATTTCCAACACATATTTATTAAGTCATCTTTGAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 18

GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGAAGTGATCTCCAGCTTATTTCCAACACATATTTATTAAGTCATCTTTGAC


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 9

GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGAAGTGATCTCCAGCTTATTTCCAACACATATTTATTAAGTCATCTTTGAC


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 10

GGTGGCAATGACTATGAGATATTTGAATCTGAAAGAACAGTTGGTCATACAGgtatgctatt ... tgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGAAGTGATCTCCAGCTTATTTCCAACACATATTTATTAAGTCATCTTTGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaagtcaccattgctgtcattcccgtactgattccatatcattttgatttgcagTTACCAGCCCCAGTGACACAGCTCAGCAATGCAGATCTCTCTTTTTGTCGAAGTGATCTCCAGCTTATTTCCAACACATATTTATTAAGTCATCTTTGAC
                                       tcatttt  CT-rich tract
                                    atatcattttgattt  TA-rich tract