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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagagttagagtcagctcatccatccatctagctagctatccctccatgaaaccgcttatcatctcgcactggtaaatcctgatgtgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG

Basic information

species Zea mays
transcript GRMZM2G059083_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059083_T04 (Zea mays), 3'ss of exon 4
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgagtagagttaga-gtcagctcatccatccat-ctagctagctatccctccatgaaaccgcttatcatctcgcactggtaaatcctgatgtg----ttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG
    |||  || | |  |  ||     ||   |   |||  |||      |    | |     | | || || | | || | | | ||| | |     ||| | |||| | ||| || || || || ||||| ||| | || || |||||||| |||||||| |||||||||||||||||||||
----gtatggtcatatattggcgtgctcacttagattagagagcagaatttagtggtatatagtcaaca-cttgtagtgattacttctgcttttctgtttccttagCTTGGAACAGGAACTGGAATAGCTCCATTCAGATCATTTTTGTGGAAAATGTTCTTTGAGGAGCACGAGGACTACAAG

upper sequence: GRMZM2G059083_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g14450.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtagagttagagtcagctcatccatccatctagctagctatccctccatgaaaccgcttatcatctcgcactggtaaatcctgat-gtgttcatc----agCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG
               || || || | | ||  | |  | | | |||  ||  | |   |  | | |   |       | || |  |||  |   |||||    |||| ||||| ||||| ||||| ||||| || ||||| ||||||||||| |||||||||||| |  | || |||||||||
---------------gtgagttc-tgcttcagtatcaccaaccatct-tctgttatgtcaatcagctgtttctttgagaaagtattgaaagcaatcatcttgcagCTTGCAACTGGTACTGGCATTGCTCCTTTTCGCTCATTCTTGTGGAAAATGTTCTTCGAGAAATATGAAGACTACAAG

upper sequence: GRMZM2G059083_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0023g03510.t01 (Vitis vinifera), 3'ss of exon 5
--gtgagtagagttagagtcagctcatccatccatctagctagctatccctccatgaaaccgcttatcatctcgcactggtaaatcctgatgtgttcat--cagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG
   | | |     |  ||     |  |||         | | |  ||   |     |||    |||       | | || || | | |||| | |||||  ||||| ||||| || || || || ||||| |||||||| ||||||||||| |||||||| ||| |||| || |||||||||
gtattattcattctccagc--atttgtcctaatgctatggttgtaatggttttccaaaatgtattagtcgtatgtattgttacaacatgatttcttcattgcagCTTGCAACTGGAACTGGAATTGCTCCTTTCCGCTCATTCTTGTGGAAAATGTTCTTTGAGAAGCATGAAGACTACAAG

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|78085944|gb|DV514337.1|DV514337
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|76935133|gb|DV174192.1|DV174192
EST:     AACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: AACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|5791146|gb|AI977938.1|AI977938
EST:     TGGG-AA-GAGATGCTCATGCCCAAAGACCCCAACGCANCAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|13150081|gb|BG320403.1|BG320403
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|211014995|gb|FL081548.1|FL081548
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|148968309|gb|EE019500.2|EE019500
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|78021596|gb|DV489983.1|DV489983
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|78085945|gb|DV514338.1|DV514338
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|13315987|gb|BG410434.1|BG410434
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|5791046|gb|AI977838.1|AI977838
EST:     ACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: ACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|13315986|gb|BG410433.1|BG410433
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|76015965|gb|DT943135.1|DT943135
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|71420120|gb|DR805018.1|DR805018
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|31405961|gb|CD484693.1|CD484693
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|6918750|gb|AW400280.1|AW400280
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|94474502|gb|EB703460.1|EB703460
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|89249821|gb|DY621607.1|DY621607
EST:     TGGCCAAGGAGATGTTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|6952551|gb|AW424619.1|AW424619
EST:     TGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGCTACCGGCATCGCTCCGTTCCGCTCCTTCTTGNGGAAGATG
genomic: TGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|13382263|gb|BG458938.1|BG458938
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAG
EST: gi|13126400|gb|BG316970.1|BG316970
EST:     TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
EST: gi|76015964|gb|DT943134.1|DT943134
EST:     GGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATG                         CTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG
genomic: TGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATG

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), 40 (downstream exon)
Score: 57

GTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 493

GTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG


Block sizes: 42 (upstream exon), 34 (downstream exon)
Score: 7

GTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 302

GTGACTTGAAGCCAGGCGCTGAGGTGAAGATCACAGGGCCAGTGGGCAAGGAGATGCTCATGCCCAAAGACCCCAACGCAACAATCATCATGgtgagtagag ... tgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctccatgaaaccgcttatcatctcgcactggtaaatcctgatgtgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG
                                     tcctgat  putative branch site (score: 302)
                ttatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtagagttagagtcagctcatccatccatctagctagctatccctccatgaaaccgcttatcatctcgcactggtaaatcctgatgtgttcatcagCTCGCAACGGGTACCGGCATCGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCTTCGAGGAGCACGAGGACTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA