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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttgtgaactgtgactttttttcactagatccactatgtgcagttagcaaaaaaaaaaaaaaactactgtttgatgtctgcattgttttgctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG

Basic information

species Zea mays
transcript GRMZM5G833124_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 3
--acttgtgaactgtgactttttttcactagatccactatgtgcagttag--caaaaaaaaaaaaaaactactgtttgatgtctgcattgttttgctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG
  ||  |||| ||   |||   | | | |   |   ||| |||| | |      | |  ||         | |||   ||      || ||||   | ||||||||||| ||||| || |||||||| |||||||||||||||||||||||||||||||| || ||||| ||||||
ataccagtgacct---actcagtatgatttagttt-ctaagtgctgatgtgttcatattaaccttttgtgattgtgctattctctgatagtttcattcctacagGATGGAGCTGGCCGAGTTGGAAAAATGCTTTTTGCCCGCCAAGGGAAGAAATTTGACTACGACCTAAAGCAG

upper sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 3
acttgtgaactgtgactttttttcactagatccactatgtgcagttagcaaaaa---aaaaaaaaaactactgtttgatgtctgcatt---gttttgctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG
    ||   |  |     | | ||  |  || ||  |||      || |||      |||| |     ||||   | ||   || ||     | |   |  |  ||||||| |||||||||||||| || |||||||||||  | || || |||||||||||||||||  |||| |||
----gttttcctttctcgtatatcctttcatgcatcatgcatgtataacaatcctttaaaacatggcttactcactcattgttgaatatcaatgtaattcttgtagGATGGTGCTGGGCGTGTTGGGAAAATGCTTTTTGCGAGGCAGGGAAAGAAATTTGATTATGATTTGAAACAG

upper sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 3
acttgtgaactgtgactttttttcactagatccactatgtgcagttagcaaaaaaaaaaaaaaactactgtttgatgtctgcattgttttgctac---tacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG
   | ||   | || | || |||    || |  | | |       | | | ||    |    || |  | |||| ||  |  |  |||    ||    | |||||||| ||||| |||||||| || ||||||||||| || ||||||||||| ||||||||||| || || |||
---tttgctttatggccttcttttttcagtttgaatttagcttcatggaataattgcatttgaaatgatatttgttgaatttaaagttacattatatgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAG

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|211214593|gb|FL385234.1|FL385234
EST:     CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAA                         GATGGNNGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCNGCCAGGGGAAGA
genomic: CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGG-GCTGGGCGTGTTGGAAAGATGCTTTTTGCCC-GCCAAGGGAAGA
EST: gi|19822663|gb|BQ048687.1|BQ048687
EST:     CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAG                         GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
genomic: CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
EST: gi|32931635|gb|CF036447.1|CF036447
EST:     CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAG                         GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
genomic: CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
EST: gi|18450494|gb|BM428772.1|BM428772
EST:     TCAAAGCAGTGTCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAG                         GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
genomic: CCAAAGCAG-GGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
EST: gi|91876063|gb|EB406020.1|EB406020
EST:     CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAG                         GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
genomic: CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
EST: gi|19822664|gb|BQ048688.1|BQ048688
EST:     CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAG                         GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
genomic: CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
EST: gi|87153939|gb|DY398728.1|DY398728
EST:     CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAG                         GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
genomic: CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
EST: gi|71440154|gb|DR821204.1|DR821204
EST:     CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAG                         GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
genomic: CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
EST: gi|18649305|gb|BM498124.1|BM498124
EST:     CAACTGGATTCTCAAG                         GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
genomic: CAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
EST: gi|32932638|gb|CF037450.1|CF037450
EST:     CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAG                         GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
genomic: CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
EST: gi|93281685|gb|EB673949.1|EB673949
EST:     CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAG                         GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA
genomic: CCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAA

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), 48 (downstream exon)
Score: 41

AGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAACTCTGTTGGAGTCTCCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

AGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAACTCTGTTGGAGTCTCCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 187

AGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAACTCTGTTGGAGTCTCCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 142

AGCAATGGGTGTGTTTACAACAAGGACCTTGCTCAACTCTGTTGGAGTCTCCCAAAGCAGGGCTGCATCTGGTGCTGTGGCTATCAACTGGATTCTCAAGgtggaaatac ... gctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcaaaaaaaaaaaaaaactactgtttgatgtctgcattgttttgctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG
                        gtttgat  putative branch site (score: 142)
                                         ttttgct  putative PPT
     aaaaaaaaaaaaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttgtgaactgtgactttttttcactagatccactatgtgcagttagcaaaaaaaaaaaaaaactactgtttgatgtctgcattgttttgctactacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - -tgaactg
- - - - - - - - - - - - - - gatccac
- - - - - - - - - - - - - - - - - - -tgtgcag
- - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtctgca