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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgccaaccggcggtctctccatccacctattcaatcgatcgaactttcgatgtttcctgtgggctagggtttctgggattccggatctgattgcttctggttgttgagtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTCCGCGTGCTTGTCACTCCCACCAGCGACCTCGGGAAGATTCTCGCCTGTA

Basic information

species Zea mays
transcript GRMZM2G147671_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147671_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g13970.2 (Oryza sativa), 3'ss of exon 2
gtgccaaccggcggtctctccatccacctattcaatcgatc-gaactttcgatgtttcctgtgggctagggtttctgggattccggatctgattgcttctggttgttgag-tgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTCCGCGTGCTTGTCACTCCCACCAGCGACCTCGGGAAGATTCTCGCCTGTA
                 | ||| |  || |  | ||||||| |  |   |   |||   || |   |||||||    ||  ||||||||||| || || |  ||   | |     ||||||| |||||||||||||| || ||||| |||||||||||||| |||||||| |||||||| ||||||||||||||||||||||| ||||| ||||| ||||
--------------gtacgccaccgtccgacccgatcgatccgcgcggccttcgttgtgtgcgatttagggttct--gggctccggatctgactgttttttttttcgggggcctttgcagTCCAACCCGGAGAACACGGTGGGCGTCATGACGATGGCCGGAAAGGGCGTGCGCGTGCTCGTCACTCCCACCAGCGACCTCGGCAAGATCCTCGCTTGTA
















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|211069192|gb|FL190617.1|FL190617
EST:     CCAGGCGCAGGCCGATTGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: CCAGGCGCAGGCCGA-TGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211071930|gb|FL190632.1|FL190632
EST:     TCCAGGCGCAGGCCGATG-CGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|31353854|gb|CD438211.1|CD438211
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211069191|gb|FL190616.1|FL190616
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211071927|gb|FL190629.1|FL190629
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|29947654|gb|CB816768.1|CB816768
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211069188|gb|FL190613.1|FL190613
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|5343122|gb|AI795532.1|AI795532
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211066454|gb|FL190609.1|FL190609
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|67041049|gb|CO467304.1|CO467304
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211047092|gb|FL234544.1|FL234544
EST:     CCAGGCGCAGGCCGATTGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: CCAGGCGCAGGCCGA-TGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|47961624|gb|CN844333.1|CN844333
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|9824997|gb|BE575199.1|BE575199
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211069187|gb|FL190612.1|FL190612
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211069189|gb|FL190614.1|FL190614
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211069197|gb|FL190622.1|FL190622
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211069199|gb|FL190624.1|FL190624
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211069196|gb|FL190621.1|FL190621
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|32915709|gb|CF020521.1|CF020521
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211069190|gb|FL190615.1|FL190615
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|31360558|gb|CD444915.1|CD444915
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211069198|gb|FL190623.1|FL190623
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211069194|gb|FL190619.1|FL190619
EST:     TCCAGGCGCAGG-CGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
EST: gi|211069200|gb|FL190625.1|FL190625
EST:     TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAG                         TCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC
genomic: TCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCGGTGCCAAGACCCAGgtgccaaccg ... gtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctagggtttctgggattccggatctgattgcttctggttgttgagtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTCCGCGTGCTTGTCACTCCCACCAGCGACCTCGGGAAGATTCTCGCCTGTA
                      atctgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgccaaccggcggtctctccatccacctattcaatcgatcgaactttcgatgtttcctgtgggctagggtttctgggattccggatctgattgcttctggttgttgagtgggtgcagTCGAACCCGGAGAACACAGTAGGCGTGATGACGATGGCCGGGAAGGGCGTCCGCGTGCTTGTCACTCCCACCAGCGACCTCGGGAAGATTCTCGCCTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA