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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtagcttacctaattagtagcagtaatctagtgttagttaggataaggtaaggtgatgtattgggtggtcgtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAG

Basic information

species Zea mays
transcript GRMZM2G059083_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059083_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT5G66190.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggtagcttacctaattagtagcagtaatctagtgttagttagga--------taaggtaaggtgatgtattgggtggtcgtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAG
    |||  |  | |||||||  |   |    | || ||  ||||            ||| |  |   ||  | || |||| |   |   ||| ||||| || || ||||| || || || || || || ||  | || ||    ||||||||||| |||||||||||||||||||| ||||| ||||| ||
----gtaaatcccttaattagggggcttttgattgtattttttagaggcatttttcgagggagagatttgattaggttggttgatgacttagGTGAGGTTCCGTATAGAGAAGGACAATCGATAGGAGTGATTCCAGAGGGAATAGACAAGAACGGGAAGCCGCACAAGCTCAGGCTTTACTCTATCGCGAG

upper sequence: GRMZM2G059083_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 3'ss of exon 2
gtaggtagcttacctaattagtagcagtaatctagtgttagttagga--------taaggtaaggtgatgtattgggtggtcgtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAG-----
    |||  |  | |||||||  |   |    | || ||  ||||            ||| |  |   ||  | || |||| |   |   ||| ||||| || || ||||| || || || || || || ||  | || ||    ||||||||||| |||||||||||||||||||| ||||| ||||| ||     
----gtaaatcccttaattagggggcttttgattgtattttttagaggcatttttcgagggagagatttgattaggttggttgatgacttaggtgagGTTCCGTATAGAGAAGGACAATCGATAGGAGTGATTCCAGAGGGAATAGACAAGAACGGGAAGCCGCACAAGCTCAGGCTTTACTCTATCGCGAGTAGTG
















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|78085945|gb|DV514338.1|DV514338
EST:     CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
EST: gi|89253046|gb|DY624832.1|DY624832
EST:     CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
EST: gi|605756|gb|T27568.1|T27568
EST:     CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATG-CG
genomic: CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
EST: gi|76015965|gb|DT943135.1|DT943135
EST:     CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
EST: gi|13490690|gb|BG517454.1|BG517454
EST:     CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
EST: gi|13557961|gb|BG549317.1|BG549317
EST:     CACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: CACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
EST: gi|13382263|gb|BG458938.1|BG458938
EST:     CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: CGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
EST: gi|13126400|gb|BG316970.1|BG316970
EST:     TGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: TGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
EST: gi|50328327|gb|CO523453.1|CO523453
EST:     GGCGACCAAGCGCCCGGGGAGACATGGCACATGGTCTTCAGCACAGAAG                         GCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG
genomic: GGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCG

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), 49 (downstream exon)
Score: 45

AAGCCCAAGGAGCCGTACGTCGGGAGGTGCCTGCTCAACACCAGGATCACCGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

AAGCCCAAGGAGCCGTACGTCGGGAGGTGCCTGCTCAACACCAGGATCACCGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAG


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 14

AAGCCCAAGGAGCCGTACGTCGGGAGGTGCCTGCTCAACACCAGGATCACCGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

AAGCCCAAGGAGCCGTACGTCGGGAGGTGCCTGCTCAACACCAGGATCACCGGCGACCAAGCGCCCGGGGAGACGTGGCACATGGTCTTCAGCACAGAAGgtaggtagct ... gtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctagtgttagttaggataaggtaaggtgatgtattgggtggtcgtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAG
        ttagtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtagcttacctaattagtagcagtaatctagtgttagttaggataaggtaaggtgatgtattgggtggtcgtgcatgcagGCGAGGTCCCCTACAGAGAGGGCCAGTCCATCGGCGTCATCGCGGATGGCGAGGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA