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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtaatctccatgcagaaattggaatgacatcatgacttcatgggttcatattatattcagtatataaactaaagcctcctgttttgtgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG

Basic information

species Zea mays
transcript GRMZM2G057329_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057329_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g59700.1 (Oryza sativa), 3'ss of exon 3
-ttttgtaatctccatgcagaaattggaatgacatcatgacttcatg-ggttcatattatattcagtatataaactaaagcctcctgttttg-tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG
      |   |      | |  |||    |  |  |||   |  ||  | ||||| | ||||| |  | ||||| ||||||   |||||||| ||||||  ||   ||||||||||||||||| |||||||| ||||||||||||||||||||||| || || ||||||||||| || ||||| || || || |||
aagcattgggcaatgaactgttattcagctatctccatacttggatttgattcatgtgatattaa--aaataaattaaagcactctgttttgatgtccta-agGGGGATGGTACTGGATGCACGTCAATCTATGGTACCAAATTTGATGATGAAAACTTCATTGCAAAGCATACTGGTCCTGGCCTACTTTCTATG

upper sequence: GRMZM2G057329_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G38730.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------ttttgtaatctccatgcagaaattggaatgacatcatgacttcatgggttcatattat--attcagtatataaactaaagcctcctgttttgtgt----cctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG
                                       ||  | || |   | |  || | | | || | |   |   || ||  |   | || |   |||  ||  ||||      | | |||  || | |      ||||||||||||||| ||||||||  |||||||||||   ||| ||||| ||||| |||||||  || || ||||| || || ||| ||||||| |||
gtcagtaccctttacttcttataaatcctcacttcttgattgcttatgttggttctcaattggcactggcttttagttctcttgtttgtgtgttcttggttcgttacttaaatctcttcttactgcattatctaatttgtgcagAATGATGGTAGTGGATGCATGTCAATCTACGGCCACAAGTTTGAGGATGAGAATTTTACTGCTAAACATACTGGACCAGGATTGCTCTCCATG
















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|211112964|gb|FL394568.1|FL394568
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211494317|gb|FL423862.1|FL423862
EST:     CCATAGAGTGATCAAAGATTTCAATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: CCATAGAGTGATCAAAGATTTCA-TGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|19058149|gb|BM736816.1|BM736816
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCACGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGNACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211023124|gb|FL428614.1|FL428614
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|19057931|gb|BM736598.1|BM736598
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGGACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|19058424|gb|BM737091.1|BM737091
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211494316|gb|FL423861.1|FL423861
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTA
EST: gi|87153432|gb|DY398221.1|DY398221
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|32858929|gb|CD998610.1|CD998610
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211452160|gb|FL396759.1|FL396759
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGG
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGG
EST: gi|211129147|gb|FL382949.1|FL382949
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|60349165|gb|DN216138.1|DN216138
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|60349812|gb|DN216785.1|DN216785
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|60394638|gb|DN227508.1|DN227508
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|24766439|gb|CA401593.1|CA401593
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATTTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211360429|gb|FL377716.1|FL377716
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211357849|gb|FL385252.1|FL385252
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|87152302|gb|DY397091.1|DY397091
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211438423|gb|FL465204.1|FL465204
EST:     TCCATAGAGTGATCAAAGATTTCATGATYCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211073855|gb|FL392646.1|FL392646
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATTATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211027097|gb|FL381991.1|FL381991
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211099687|gb|FL379428.1|FL379428
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|22490292|gb|BU050215.1|BU050215
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211206179|gb|FL469079.1|FL469079
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211048939|gb|FL421705.1|FL421705
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAAT
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAAT
EST: gi|8577336|gb|BE129973.1|BE129973
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211433999|gb|FL392548.1|FL392548
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|12047274|gb|BF729413.1|BF729413
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCCCATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211254561|gb|FL409666.1|FL409666
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|78179385|gb|DV549758.1|DV549758
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|60398036|gb|DN230852.1|DN230852
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
EST: gi|211523932|gb|FL381031.1|FL381031
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTA
EST: gi|211042680|gb|FL406379.1|FL406379
EST:     TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAG                         AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA
genomic: TCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAA

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: 272

AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 145

AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 200

AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

AAAAAATGCTTTGCCACAAGGTTATAAGGGCTGCCAATTCCATAGAGTGATCAAAGATTTCATGATTCAGGGTGGTGACTTCTTGAAGgtttgtatgc ... tgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggttcatattatattcagtatataaactaaagcctcctgttttgtgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG
                         aactaaa  putative branch site (score: 135)
      atattatattcagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtaatctccatgcagaaattggaatgacatcatgacttcatgggttcatattatattcagtatataaactaaagcctcctgttttgtgtcctgcagAATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - tccatgc
- - - - - - - - - - - - - - - - - - - -cttcatg
- - - - - - - - - - - - - - - - - - - - - - - - ttcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa