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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatttttttataagactccaatgtacattttctaaattgtgtgccagaagaattgaaatttagttgttttaatgtttgaatttgttttctgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCGTGCAACAAAAGAG

Basic information

species Zea mays
transcript GRMZM2G169095_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169095_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g33330.1 (Oryza sativa), 3'ss of exon 10
-----taatttttttataagactccaatgtacattttctaaattgtgtgccagaagaattgaaatttagttgttttaatgtttgaatttgttttctgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCGTGCAACAAAAGAG
     | ||||  |      | |  |  |   |      || |  | |    ||| ||| |     |     |||   ||||   |||| | |||  | |||||| | |   |||||||||||||| ||||||||||| ||||||||||| ||||||||| | ||||||
acacatcatttggtctatgcattatacggagtagcaatcaattattatttatgaacaatgg-----tgtgcatttggttgttaatatttttgttcactcctgtagGGAAGTAAAACTTACTGAGGTTTCTGTGAGTGATAAACTTGAAGGTTTCCGTGCATCTAAAGAG

upper sequence: GRMZM2G169095_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g33340.1 (Oryza sativa), 3'ss of exon 10
---taatttttttataa--gactccaatgtacattttctaaattgtgtgccagaagaattgaaatttagttgttttaatgtttgaatttgttttctgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCGTGCAACAAAAGAG
   ||||   |  ||||  |    ||||    |||| ||  ||| | |   |  || | ||   |  | |||| |||||  |  | |||  ||||  | |||||| | |   |||||||||||||| ||||||||||| ||||||||||| ||||||||  | ||||||
gtttaatacatgcataatggcaatcaattgttatttgctttattatatatgaacagtagtg---tgcatttgtgttaataat--atttttgtttcactcctgtagGGAAGTAAAACTTACTGAGGTTTCTGTGAGTGATAAACTTGAAGGTTTCCGTGCCGCTAAAGAG

upper sequence: GRMZM2G169095_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g45360.1 (Oryza sativa), 3'ss of exon 8
-------taatttttttataagactccaat-gtacattttctaaattgtgtgccagaagaattgaaatttagttgttttaatgtttgaatttgttttctgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCGTGCAACAAAAGAG
       ||    || ||| |  |    || || || ||| | |||| ||      || | |    |||| ||||| |||||||||    ||||||    | ||||||       |||||||| ||||| |||||||| || ||||||||||| ||||||||| | ||||||
tttgttctatgcattatattaatcaattatcgtccactttattaattatgaat---aatagtgtgcatttggttgtgttaatgttt----ttgtttcac-tcctgtagGAATGTAAAACTTACAGAGGTTTCTGTGAGCGATAAACTTGAAGGTTTCCGTGCATCTAAAGAG

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|211292033|gb|FL028321.1|FL028321
EST:     GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTT                         AGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCCTCCG
genomic: GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTTgtgagtttat ... tgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
EST: gi|50323429|gb|CO518555.1|CO518555
EST:     GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTT                         AGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
genomic: GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTTgtgagtttat ... tgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
EST: gi|32833772|gb|CD973450.1|CD973450
EST:     GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTT                         AGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
genomic: GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTTgtgagtttat ... tgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
EST: gi|67031560|gb|CO460309.1|CO460309
EST:     GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTT                         AGCAACCAAACTTACTGANGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
genomic: GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTTgtgagtttat ... tgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
EST: gi|33102339|gb|CF062299.1|CF062299
EST:     GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTT                         AGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
genomic: GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTTgtgagtttat ... tgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
EST: gi|67018778|gb|CO447527.1|CO447527
EST:     GCTTCTGGTTATTTCAGTGAGATAAAAGTGTCGCATAAAAATGAACATTT                         AGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
genomic: GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTTgtgagtttat ... tgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
EST: gi|32834344|gb|CD974022.1|CD974022
EST:     GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTT                         AGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
genomic: GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTTgtgagtttat ... tgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
EST: gi|211292032|gb|FL028320.1|FL028320
EST:     GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTT                         AGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGA
genomic: GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTTgtgagtttat ... tgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGA
EST: gi|32937410|gb|CF042229.1|CF042229
EST:     GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTT                         AGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG
genomic: GCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTTgtgagtttat ... tgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCG

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), 49 (downstream exon)
Score: 162

ATGCAGGAGAACTATGGAGCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTTgtgagtttat ... tgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCGTGCAACAAAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

ATGCAGGAGAACTATGGAGCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTTgtgagtttat ... tgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCGTGCAACAAAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

ATGCAGGAGAACTATGGAGCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTTgtgagtttat ... tgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCGTGCAACAAAAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

ATGCAGGAGAACTATGGAGCTTCTGGTTATTTCAGTGAGATAAAAGGGTCGCATAAAAATGAACATTTgtgagtttat ... tgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCGTGCAACAAAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaagaattgaaatttagttgttttaatgtttgaatttgttttctgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCGTGCAACAAAAGAG
                      ttttaat  putative branch site (score: 301)
                                    tttgttttctgttct  putative PPT
           aaatttagttgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatttttttataagactccaatgtacattttctaaattgtgtgccagaagaattgaaatttagttgttttaatgtttgaatttgttttctgttctgtagAGCAACCAAACTTACTGAGGTGTCTGTGAGTGACAAACTTGAAGGCTTCCGTGCAACAAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - tacattt
- - - - - - - - - - - - - - - - - - - - - - -cagaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgtttg