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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattctgcatatatgtaacataattcagcagtttgtgtattgcgcttgtttccccattgaatttcactattagttgattacgaagtcattattgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGGTATGATCCATGTCA

Basic information

species Zea mays
transcript GRMZM2G018177_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018177_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g05490.1 (Oryza sativa), 3'ss of exon 3
cattctgcatatatgtaacataattcagcagtttgtgtattgcgcttgtttccccattgaatttcactattagttgattacgaa---gtcattattgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGGTATGATCCATGTCA
   |||  |||   ||       || ||  |    | ||   |  |         | | |  ||   | | ||||| ||   ||    | ||| || |||||| ||||||||||| ||||||||| |  |||||||||| |||||||||||||||||||||||   | || |||| ||||||||||||               
---tctcaatagccgtcttcgcttttaggcgaggttataagccattcaccattgaactcatcttttgtttaagttggttgttaatctattatttttaatgcagCGCTGAGATGCTTGTCAACCTTAGTATTCCCTGGGTTATTCTTGGACACTCTGAAAGGAGGAGTTTGTTGGGTGAATCAAATGAG---------------
















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|211510433|gb|FL122509.1|FL122509
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|211239820|gb|FL120927.1|FL120927
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAAATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|32915076|gb|CF019888.1|CF019888
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|211242055|gb|FL120940.1|FL120940
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGG
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGG
EST: gi|211239823|gb|FL120930.1|FL120930
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAAATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTG
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTG
EST: gi|211244297|gb|FL120959.1|FL120959
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAAATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|211242063|gb|FL120948.1|FL120948
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGT
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGT
EST: gi|76014494|gb|DT941664.1|DT941664
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|211242068|gb|FL120953.1|FL120953
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAAATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|211326721|gb|FL104662.1|FL104662
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAA-TTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|211244293|gb|FL120955.1|FL120955
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|211510425|gb|FL122501.1|FL122501
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|211244299|gb|FL120961.1|FL120961
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAAATGCTCGTCAACCTTGG
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGG
EST: gi|211242061|gb|FL120946.1|FL120946
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCCTGGGTCATTCTTGGACACT
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCC-TGGGTCATTCTTGGACACT
EST: gi|13515655|gb|BG517931.1|BG517931
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAG                         TGCTGAGATGCTCGGCAACCTTGGCGTTCCCTGGGTCATTCTTG
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTG
EST: gi|37419500|gb|CF647433.1|CF647433
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
EST: gi|13388321|gb|BG462272.1|BG462272
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTG
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTG
EST: gi|211510424|gb|FL122500.1|FL122500
EST:     GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACTGGTGAAATTAG                         TGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC
genomic: GCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTC

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: 387

TGTTCCTCCCGGTGGTCAAGAGCCAGCTGCGCCAAGAGTTCCAAGTTGCTGCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGGTATGATCCATGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 694

TGTTCCTCCCGGTGGTCAAGAGCCAGCTGCGCCAAGAGTTCCAAGTTGCTGCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGGTATGATCCATGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 717

TGTTCCTCCCGGTGGTCAAGAGCCAGCTGCGCCAAGAGTTCCAAGTTGCTGCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGGTATGATCCATGTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 453

TGTTCCTCCCGGTGGTCAAGAGCCAGCTGCGCCAAGAGTTCCAAGTTGCTGCTCAGAACTGCTGGGTGAAGAAGGGAGGTGCATTCACCGGTGAAATTAGgttagtcttt ... attgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGGTATGATCCATGTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttccccattgaatttcactattagttgattacgaagtcattattgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGGTATGATCCATGTCA
                                            tattgat  putative branch site (score: 453)
          attgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattctgcatatatgtaacataattcagcagtttgtgtattgcgcttgtttccccattgaatttcactattagttgattacgaagtcattattgatgcagTGCTGAGATGCTCGTCAACCTTGGCGTTCCCTGGGTCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGGTATGATCCATGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - ctgcata
- - - - - - - - aacataa
- - - - - - - - - - - - tcagcag
- - - - - - - - - - - - - - - - - -tgtattg