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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaccgagaacaatcatgagacctgccgtactttttcgcatgctttgtttttttttgtgtgtaaagctggaagttttgttctgtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG

Basic information

species Zea mays
transcript GRMZM2G005493_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 16
gtaataaccgagaacaatcatgagacctgccgtactttttcgcatgcttt-gtttttttttgtgtgtaaagctggaagttttgt-----tctgtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG
                        | |||  | || ||   || | ||   |||||| ||   |  |  || || ||  ||| |     | | || ||||||||||||||||| ||||  || || |||||||| |||||||| |||||||||||||| ||||||||||| |||
----------------------gtaactg--gaacattacagccttctaaagtttttattcagggatctagatgtaatctttttatctctttctgctgttagGATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGTGAGATCGGTGCCTTGATTGAG
















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|60337180|gb|DN204153.1|DN204153
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|29130773|gb|CB381477.1|CB381477
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|76286922|gb|DV026490.1|DV026490
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|113684811|gb|DW837585.1|DW837585
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAG
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAG
EST: gi|3157115|gb|AA979737.1|AA979737
EST:     CCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: CCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|60344318|gb|DN211291.1|DN211291
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|32836432|gb|CD976110.1|CD976110
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCACAAGCGGTA
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTA
EST: gi|211379703|gb|FL400539.1|FL400539
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCC-CCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|32844741|gb|CD984422.1|CD984422
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|32845281|gb|CD984962.1|CD984962
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|211141141|gb|FL467349.1|FL467349
EST:     GAATGGACACCYTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGT-CGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|213179445|gb|FM183428.1|FM183428
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|33097350|gb|CF057310.1|CF057310
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|32856567|gb|CD996248.1|CD996248
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|32838372|gb|CD978050.1|CD978050
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTA
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTA
EST: gi|32845336|gb|CD985017.1|CD985017
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGT
EST: gi|37385849|gb|CF630089.1|CF630089
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGC
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|60346929|gb|DN213902.1|DN213902
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|32935034|gb|CF039846.1|CF039846
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTA
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTA
EST: gi|33101201|gb|CF061161.1|CF061161
EST:     GGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|211459151|gb|FL411539.1|FL411539
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|32844417|gb|CD984098.1|CD984098
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGT
EST: gi|60337495|gb|DN204468.1|DN204468
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|67037452|gb|CO464268.1|CO464268
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTNCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|32844874|gb|CD984555.1|CD984555
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|6012630|gb|AW062067.1|AW062067
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|32838758|gb|CD978439.1|CD978439
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTA
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGG-TTCCCTAGATGCTCTCGTCCGCAAGCGGTA
EST: gi|60353702|gb|DN220675.1|DN220675
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|110219847|gb|EC901745.1|EC901745
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTTTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|74244418|gb|DT652332.1|DT652332
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|110213725|gb|EC895622.1|EC895622
EST:     GAATGGACAACCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
EST: gi|32837235|gb|CD976913.1|CD976913
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTA
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTA
EST: gi|60347419|gb|DN214392.1|DN214392
EST:     GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAG                         GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT
genomic: GAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGT

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: 792

GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1103

GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 796

GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1338

GCGGAGGGAAAGCACTGATGTTGAGGACTTGTTTCTTGCTCATATCTCCGGAATGGACACCCTGGCCCGTGGCCTCCGCAACGCCGCCAAGCTGATCGAGgtaataaccg ... gtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgctttgtttttttttgtgtgtaaagctggaagttttgttctgtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG
      tttgtttttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataaccgagaacaatcatgagacctgccgtactttttcgcatgctttgtttttttttgtgtgtaaagctggaagttttgttctgtgatgttagGATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT