Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctgaactgttctaaatgtgtcacggattgctttcaggttctctttccagatcacaatttaattatttaatttcttgtttatttttttatcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG

Basic information

species Zea mays
transcript GRMZM2G075485_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 3'ss of exon 1
gtctgaactgt-tctaaatgtgtcacggattgct----ttcaggttctctttccagatcacaatttaattatttaatttcttgtttatttttttatcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG
  || || |   | |  |      |   |||| |    ||||| ||    || |   | | ||   || ||  | ||||  |||||  ||| ||    | |||||||  |||| ||||||| ||| ||||| || || |||||||||||||| |||||||| |||||  | || || || ||||| ||||||||||| ||||||
--ctaaagtacatatgcaatcagaaacaattgttatgcttcagttttgtctttct--ttataacacaagtaactcatttgatgtttcctttcttcat-tctgaagATCTTAGGGGTTGAGAGGACAGCTTCACAGCAGGAAATAAAGAAGGCTTATCACAAGTTGGCCTTACGTCTTCATCCAGACAAGAATCCTGGAGATGAG

upper sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA19G32480.1 (Glycine max), 3'ss of exon 1
---------------------gtctgaactgttctaaatgtgtcacggattgctt------tcaggttctctttccagatcacaatttaattatttaatttctt-gtttat---ttttttatcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG-
                      | |     | | |   |   | | |||||  ||      |||  |||  ||  |   |    | |    ||| | ||  ||| ||||     |  || |    ||| || |||| || || ||||  || || ||||| || |||||||||||||||||  |||| |||||  |||| || ||||| |||||||| ||||| |||||  
gtaccctaaaaaattcatgctttttctttcgctttcctttgataatggattatttcactattcaaattcaattcgcgtgttgttactgtgatatattatgactttgtttgacggtggttgagtggttgtagGTTCTTGGCGTGGAGAGAACGGCGTCTCAGCAGGAAATAAAGAAGGCGTACTACAAGTTGGCGTTGCGGCTTCACCCCGATAAGAACCCTGGTGATGATG
















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|211337601|gb|FL103353.1|FL103353
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|78117499|gb|DV535886.1|DV535886
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|78116316|gb|DV534703.1|DV534703
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211337600|gb|FL103352.1|FL103352
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211339984|gb|FL103354.1|FL103354
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211342376|gb|FL103369.1|FL103369
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211339995|gb|FL103365.1|FL103365
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211337599|gb|FL103351.1|FL103351
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|91870824|gb|EB401103.1|EB401103
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211339988|gb|FL103358.1|FL103358
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAG-CTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211339990|gb|FL103360.1|FL103360
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211342377|gb|FL103370.1|FL103370
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211339987|gb|FL103357.1|FL103357
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211339985|gb|FL103355.1|FL103355
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAARGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211337598|gb|FL103350.1|FL103350
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGTGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211339993|gb|FL103363.1|FL103363
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|32909541|gb|CF014353.1|CF014353
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|71443604|gb|DR824654.1|DR824654
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211337592|gb|FL103344.1|FL103344
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|60341956|gb|DN208929.1|DN208929
EST:     ATGGCTGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211342378|gb|FL103371.1|FL103371
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGTGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211339992|gb|FL103362.1|FL103362
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211337591|gb|FL103343.1|FL103343
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211339989|gb|FL103359.1|FL103359
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211337597|gb|FL103349.1|FL103349
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211339997|gb|FL103367.1|FL103367
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
EST: gi|211025378|gb|FL421223.1|FL421223
EST:     ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAG                         ATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT
genomic: ATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTAT

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 1 RNA-Seqlibrary.


Block sizes: 12 (upstream exon), 38 (downstream exon)
Score: 2

GGGCCGCAAGGCTAGGGTTTCGCACGACGCCGACGCCGACGCCGACGCCGATGGCAGCGAGGATGAGAGGGCCACCACTGCGGGCAGGAGCCTCTACGAGgtaaggcgcc ... tcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccagatcacaatttaattatttaatttcttgtttatttttttatcatttgaagATTCTAGGAGTTGAGAAGACCGCTTCTCAACAAGAAATAAAGAAGGCGTATCACAAATTGGCTCTGCGCCTCCACCCAGATAAGAATCCTGGGGATGAG
                    atttaat  putative branch site (score: 2)
                          tttcttgtttattttt  CT-rich tract
           aatttaattatttaat  TA-rich tract