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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgtggattgaaatttgacgttttctaccacattttttttccagaaaaactgcttagatttgctgctatgtcatcctctttatactttttttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG

Basic information

species Zea mays
transcript GRMZM2G382104_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g58750.1 (Oryza sativa), 3'ss of exon 8
---acgtggattgaaatttgacgttttctaccacattttttttccagaaaaactgcttagatttgctgctatgtcatcctctttatactttttttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG
   |||| | |  || |||| | |  |  |  |  |||     |||       |   | | | ||||| |   | ||||  | | | | || |||  ||||||||||| |||||||||||||| ||||| ||||||||||| ||||||||||| |||||||||||||||||||||||||| ||||| ||  || |||| ||||
tatacgtagttgaaactttgtcatgctgaatga--tttagcaaccatcctcgttatattgttatgctgttgcatgatccattgttttccttgtttg-ctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAGAAGAAGGGTGACAATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTG

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA05G37870.1 (Glycine max), 3'ss of exon 10
-acgtggattgaaatttgacgttttctaccacattttttttccagaaaaactgcttagatttgctgcta--tgtcatcctctttatactttttttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG
 | ||   || | ||||    | || ||      | ||||||||   | | ||  |  |   | ||     ||   || |  || || |||  | |   |||||| || || || ||||||||||| |||||||| || |||||||||||||| ||||| || ||   ||||||||| || ||||||||||   |||| ||||
tatgtcttttcacatttc---tattataatgacctgtttttccatgtagattggctgaacaggttgtccactgatttctttattttattttcctatcaagcagCTTTCATTCCAAATGTGGACGAACCAGATGCAGGAAACGTTGAACTCAAAGAAGAAAGGGGATGCTGCTTTTCGGCACAAGGATTTTAAAACTGCAATTG

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G01730.1 (Glycine max), 3'ss of exon 10
-acgtggattgaaatttgacgttttctaccacattttttttccagaaaaactgcttagatttgctgctatgtcatcctctttatactttttttttct---gcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG
 | ||   || | |||||   | |  ||      | ||||||||   | ||||  |  ||    || |   | ||  |||||||    ||||  | |   |||||| || || || ||||||||||| |||||||| || || ||||||||||| ||||| || |||  ||||||||| || ||||||||||   |||| ||||
tatgtcttttcacatttg---tatcatattgacctgtttttccatgtagactggctgaatggattgttccctgatt-tctttatttcgttttcctatcaagcagCTTTCATTCCAAATGTGGACGAACCAGATGCAGGAAACATTGAACTCAAAGAAGAAAGGGGACGCTGCTTTTCGGCACAAGGATTTTAAAACTGCAATTG

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 9
lower sequence: AT4G00710.1 (Arabidopsis thaliana), 3'ss of exon 9
------------acgtggattgaaatttgacgttttctaccacattttttttccagaaaaactgcttagatttgctgctatgtcatcctctttatactttttttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG
            |  |   ||| ||      ||  | |  | | | ||  |    ||| |  | |||   |        |||   |    ||  |    |||     |||||||||| ||||| ||||||||  | |||||||||||  | |||||||| || |||||||||||    |||||  | || || || ||||  |  ||||| |
gtaccttttcagaattatgttggaagaatcagtggtttggctc-tgttaatcagtgaatagtttctttcttggttcttcatggtgttgcgttactttggtttggcaatgcagCTCTCGTTTCATATGTGGACAGACCAGATGCAAGAGTCTTTGAACTCGAAGAAGAAGGGTGATGTGGCTTTCAGGCAAAAAGACTTTAGAGAGGCCATCG

upper sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 10
acgtggattgaaatttgacgttt-tctaccacattttttttccagaaaaactgcttagatttgctgctatgtcatcctctttatactttttttttct-gcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG
   |  |||| ||   ||  | | || ||    ||   |        |    ||    |  |  | |   ||| | ||  ||||  ||||| |  || |||||| || || ||||||||||| || ||||||||||| || ||||||||||| || ||||||||   |||||| || || || |||||||  ||||| ||||
-gttaaattggaaccagatctgtgtccactttgttaaatggtgtagtatcaggcactaagcta-tacatggtcttgctaattattgtttttctagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAGAAAAAGGGTGATGTTGCTTTCCGGCACAAAGATTTTAGAGCTGCAATTG

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|60350162|gb|DN217135.1|DN217135
EST:     AAATTCTAGAAAAGACAGGCTACAAGGATGATGAGGGAACTGCAAATGAG                         CTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAA
genomic: AAATTCTAGAAAAGACAGGCTACAAGGATGATGAGGGAACTGCAAATGAGgttcgtttta ... ttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAA
EST: gi|149104410|gb|EE289855.2|EE289855
EST:     AAATTCTAGAAAAGACAGGCTACAAGGATGATGAGGGAACTGCAAATGAG                         CTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAA
genomic: AAATTCTAGAAAAGACAGGCTACAAGGATGATGAGGGAACTGCAAATGAGgttcgtttta ... ttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAA
EST: gi|88749210|gb|DY533351.1|DY533351
EST:     GAAAAGACAGGCTACAAGGATGATGAGGGAACTGCAAATGAG                         CTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAA
genomic: GAAAAGACAGGCTACAAGGATGATGAGGGAACTGCAAATGAGgttcgtttta ... ttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAA

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), 48 (downstream exon)
Score: 186

TTCCCCTCTTGCCGAAGCTTGTTCCAGAAAGGATCTGACAGCAATACATGAAATTCTAGAAAAGACAGGCTACAAGGATGATGAGGGAACTGCAAATGAGgttcgtttta ... ttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 99

TTCCCCTCTTGCCGAAGCTTGTTCCAGAAAGGATCTGACAGCAATACATGAAATTCTAGAAAAGACAGGCTACAAGGATGATGAGGGAACTGCAAATGAGgttcgtttta ... ttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 106

TTCCCCTCTTGCCGAAGCTTGTTCCAGAAAGGATCTGACAGCAATACATGAAATTCTAGAAAAGACAGGCTACAAGGATGATGAGGGAACTGCAAATGAGgttcgtttta ... ttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

TTCCCCTCTTGCCGAAGCTTGTTCCAGAAAGGATCTGACAGCAATACATGAAATTCTAGAAAAGACAGGCTACAAGGATGATGAGGGAACTGCAAATGAGgttcgtttta ... ttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaactgcttagatttgctgctatgtcatcctctttatactttttttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG
                       tgtcatcctctttata  CT-rich tract
                               tctttatacttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgtggattgaaatttgacgttttctaccacattttttttccagaaaaactgcttagatttgctgctatgtcatcctctttatactttttttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC