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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttttgcaatgcttgataaagcattcattttagtttgtagcacgtgaaacttaagtctatgtttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTTTTGCAAGGGCTGCTGAAGTATGATCCATCAAGCCGTTTAACAGCACGAG

Basic information

species Zea mays
transcript GRMZM2G179308_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179308_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 10
gtatgtttttgcaatgcttgataaagcattcat--tttagtttg--tagcacgtgaaacttaagtctatgtt-tatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTTTTGCAAGGGCTGCTGAAGTATGATCCATCAAGCCGTTTAACAGCACGAG
||||| |||    || |  | |||  |||||||  | || | ||  |   || |||| || |   || | || |    |||||| ||||||||||||||||| |||||  |||  || || |||||||||||||||||||| ||| | | |||||||||| | |||||  ||||||||| ||
gtatgatttccatat-caagttaatacattcatcgtctattatgtttgatacatgaatctgattgctttattcttcatgcagAATCTGGTGATGCAAAATGTAGATCATTCTGGGGGCGAGTTCATTGACCTTTTGCAAGGTCTGTTAAGGTATGATCCAGCTAGCCGCCTAACAGCACAAG

upper sequence: GRMZM2G179308_T04 (Zea mays), 3'ss of exon 7
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 11
---------------------------------------------------------gtatgtttttgcaatgcttgataaa-gcattcattttagtttgtagcacgtgaaacttaagtctatgt---ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTTTTGCAAGGGCTGCTGAAGTATGATCCATCAAGCCGTTTAACAGCACGAG
                                                         | | ||  |     ||    |  || |  |  |||||    |   |     |   || || | | | |   |  | ||||||| || || |||||| ||||||||||  |||| |||||| | ||||||||||||||||| || || | |||||| || || | | |  | ||||| | ||
gtgtgtacttatggttttatggctttagcattgttttgttttttcaattccatatttgaaggtcctcattgtgaaaaacgaatgggtctattttttactcctgttttagtttctcaaatttgtttgcttccttggcagAATCTAGTTATGCAACATGTGGATCATTCTGCCGGAGATCTTATTGACCTTTTGCAAGGTCTTCTTAGGTATGACCCTTCCAACAGACTCACAGCTCAAG
















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|32807402|gb|CD959636.1|CD959636
EST:     GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
genomic: GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
EST: gi|32787565|gb|CD936467.1|CD936467
EST:     GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGATCAGGCTGCAGGAGATTTCATTGACCTT
genomic: GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
EST: gi|45568628|gb|CK986157.1|CK986157
EST:     GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGATCAGGCTGCAGGAGATTTCATTGACCTT
genomic: GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
EST: gi|76015336|gb|DT942506.1|DT942506
EST:     GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
genomic: GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
EST: gi|71756384|gb|DR954321.1|DR954321
EST:     GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
genomic: GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
EST: gi|211191418|gb|FL472415.1|FL472415
EST:     GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
genomic: GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
EST: gi|76015337|gb|DT942507.1|DT942507
EST:     GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
genomic: GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
EST: gi|211241890|gb|FL451479.1|FL451479
EST:     GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
genomic: GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
EST: gi|60357877|gb|DN224850.1|DN224850
EST:     GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
genomic: GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
EST: gi|33096467|gb|CF056461.1|CF056461
EST:     GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
genomic: GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
EST: gi|60347445|gb|DN214418.1|DN214418
EST:     GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT
genomic: GCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTT

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: 226

GCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTTTTGCAAGGGCTGCTGAAGTATGATCCATCAAGCCGTTTAACAGCACGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 169

GCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTTTTGCAAGGGCTGCTGAAGTATGATCCATCAAGCCGTTTAACAGCACGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 215

GCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTTTTGCAAGGGCTGCTGAAGTATGATCCATCAAGCCGTTTAACAGCACGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 142

GCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgttttt ... ttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTTTTGCAAGGGCTGCTGAAGTATGATCCATCAAGCCGTTTAACAGCACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagcattcattttagtttgtagcacgtgaaacttaagtctatgtttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTTTTGCAAGGGCTGCTGAAGTATGATCCATCAAGCCGTTTAACAGCACGAG
     attcattttagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttttgcaatgcttgataaagcattcattttagtttgtagcacgtgaaacttaagtctatgtttatgggcagAACCTGGTGATGCAAAATGTGGATCAAGCTGCAGGAGATTTCATTGACCTTTTGCAAGGGCTGCTGAAGTATGATCCATCAAGCCGTTTAACAGCACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG