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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtattttccatttgtgctcccatcgatctgtttcttctacttattcttgttatctgctaattcatttggttttaacaaaatttatcattcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG

Basic information

species Zea mays
transcript GRMZM2G118316_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118316_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g07060.1 (Oryza sativa), 3'ss of exon 4
---------ttgtattttccatttgtgctcccatcgatctgtttcttctacttattcttgttatctgctaattcatttggttttaacaaaatttatcattcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGA---TGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG
          ||| ||| | |  | |  |    ||    ||||||| |||| | | | | |||| |  || |  |    |||||||| ||| | || || |||| ||||||||||||||| |||||||||||||||||||||||   ||||||||||||||| | ||||||||||||| | | |||||| |||
ctcaataacctgtgtttgctaggtatatttttgtc----tgtttct-ctacatttccct-ttattttttactcaa---agttttaactaaactgattatgcttccccagCTCGCAAAGAAATTCCATCCTGATACTAATAAAGAAGATGCTGATGCAGAAAAGAAATTTCAAGAAGTTCAGCATGCCTACGAG

upper sequence: GRMZM2G118316_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv13s0064g01360.t01 (Vitis vinifera), 3'ss of exon 4
---ttgtattttccatttgtgctcccatcgatctgtttcttctacttattcttgttatctgctaattcatttggttttaacaaaatttatcattcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCT---GATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG
   |  |   ||  |||     || |    ||  |    ||  |  | |  ||  |   ||   | |  ||    |||  |   | ||  |||| || |  |||| ||||||||||||||||||||||| |||||||| | |   ||||| || ||||  |||||||| ||| |    || ||||||
gcctcctggattaaattatctttcacccaaattagaggattgaagatttatttcattcttgtccagttcttgatatttttc---actttgcattattatttagCTTGCAAAGAAGTTCCATCCTGATACCAATAAAGAGGATCCAGATGCCGAGAAAAAGTTTCAAGAGGTTCAAAAGGCATATGAG
















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|76922542|gb|DV169052.1|DV169052
EST:     GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
genomic: GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|74237423|gb|DT645337.1|DT645337
EST:     GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCAT-T-ATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
genomic: GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|149101262|gb|EE187374.2|EE187374
EST:     GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
genomic: GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|78088193|gb|DV516586.1|DV516586
EST:     GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
genomic: GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|93017256|gb|EB642776.1|EB642776
EST:     GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
genomic: GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|211523404|gb|FL361945.1|FL361945
EST:     GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGATGATGCAGAAAAA
genomic: GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|71757145|gb|DR955082.1|DR955082
EST:     GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
genomic: GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|211149678|gb|FL347659.1|FL347659
EST:     GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
genomic: GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|71771526|gb|DR969463.1|DR969463
EST:     GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
genomic: GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|71427931|gb|DR808981.1|DR808981
EST:     GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
genomic: GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|91049687|gb|EB160105.1|EB160105
EST:     GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
genomic: GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|34391167|gb|CF384395.1|CF384395
EST:     CGGATATAAAGAAGGCATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGATGATGCAGAAAAA
genomic: CGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|211533908|gb|FL308317.1|FL308317
EST:     CATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGATGATGCAGAAAAA
genomic: CATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|91049823|gb|EB160241.1|EB160241
EST:     GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
genomic: GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
EST: gi|71769072|gb|DR967009.1|DR967009
EST:     GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCG                         CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA
genomic: GAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 251

CCACAAGGCGGGTGTATACAAGGGATTACTATGATGTGCTTGGAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

CCACAAGGCGGGTGTATACAAGGGATTACTATGATGTGCTTGGAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 173

CCACAAGGCGGGTGTATACAAGGGATTACTATGATGTGCTTGGAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 337

CCACAAGGCGGGTGTATACAAGGGATTACTATGATGTGCTTGGAGTAAGCAAGGATGCTTCTGCACCGGATATAAAGAAGGCATATTATGCGgtatggactt ... tcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgttatctgctaattcatttggttttaacaaaatttatcattcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG
                          ttttaac  putative branch site (score: 337)
                                     tttatcattcttctcc  putative PPT
              taattcatttggtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtattttccatttgtgctcccatcgatctgtttcttctacttattcttgttatctgctaattcatttggttttaacaaaatttatcattcttctccagCTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
-tgtattt
- - - - -ccatttg
- - - - - - - - tgctccc
- - - - - - - - - - - - - - - tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - tctgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa