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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAGAAGGCGTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCGCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaaccaaacaaccctatatattacacatatatattcgcttcagtcattcccctctctttttttttgttacctaattcttcctagctactactac...

Basic information

species Zea mays
transcript GRMZM2G071620_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071620_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g54170.1 (Oryza sativa), 5'ss of exon 1
TCAAGAAGGCGTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCGCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaaccaaacaaccctatatattacacatatatattcgcttcagtcattcccctctctttttttttgttacctaattcttcctagctactactac--
|||||||||| ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| ||| ||||| |  ||    |  | | |   ||  ||  |   |  ||  | |  | ||     |||||    ||   | ||||       || | |  | | |    
TCAAGAAGGCCTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCCCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCCTCCTCATCCAAgtaaacccactgcccctctc-actcatctcagcttcctcctc-ttcccctaatcaaattctctcaacttgcttaacctgcactccccaaaccgcaatttgct

upper sequence: GRMZM2G071620_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv01s0010g03900.t01 (Vitis vinifera), 5'ss of exon 1
TCAAGAAGGCGTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCGCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaaccaaacaaccctatatattacacatatatattcgcttcagtcattcccctctctttttttttgttacctaattcttccta--gctactactac--
|||||||||||||||| || ||  | ||||||||||||||||| || ||| || |||||||| |    ||    |||||| ||||||       |||   ||||| | ||   | ||    | |  |   | |  || ||| | | ||   | |  | | || |          ||  |         |  |  | |  |    
TCAAGAAGGCGTACGAACTTTCGGTGCTCTGCGACGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAACTCTACGAGTTCTGCAGTAGCTCGAGgtaataacacaggaaaaga--aaaagtagaaaacctaaatttgatacaa--acttgcttttcataacacaaaacacaaagcaagagaaaaggaaattgttctct
















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|148980769|gb|EE027337.2|EE027337
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|78104753|gb|DV523171.1|DV523171
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|21331630|gb|BQ487011.1|BQ487011
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|211444422|gb|FL322992.1|FL322992
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|78085639|gb|DV514032.1|DV514032
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|31909804|gb|CD651102.1|CD651102
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|211399635|gb|FL347339.1|FL347339
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|71436647|gb|DR817697.1|DR817697
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|50326015|gb|CO521141.1|CO521141
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|211530058|gb|FL388005.1|FL388005
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|71448410|gb|DR829460.1|DR829460
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|101383824|gb|EB813967.1|EB813967
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|93016628|gb|EB642148.1|EB642148
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|71436011|gb|DR817061.1|DR817061
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|50325855|gb|CO520981.1|CO520981
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|31558053|gb|CD527265.1|CD527265
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|211467003|gb|FL313839.1|FL313839
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|30031661|gb|CB833512.1|CB833512
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
EST: gi|76285216|gb|DV024784.1|DV024784
EST:     GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGA                         TCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA
genomic: GTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGA

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 3 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 87

TCAAGAAGGCGTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCGCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG


Block sizes: 16 (upstream exon), 44 (downstream exon)
Score: 2

TCAAGAAGGCGTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCGCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG


Block sizes: 31 (upstream exon), 44 (downstream exon)
Score: 17

TCAAGAAGGCGTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCGCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaac ... ttaataccagTCTGCTTAAGACTCTAGAGCGGTACCAGAGGCACATCTATGCTTCAGCTGATGCTGCAGTGCCATCTAGCGATGAGATGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAGAAGGCGTACGAGCTCTCCATCCTCTGCGACGCCGAGGTCGCGCTCGTCCTCTTCTCCCACGCCGGCCGCCTCTACCAGTTCTCATCCTCCTCCGAgtaatcaaaccaaacaaccctatatattacacatatatattcgcttcagtcattcccctctctttttttttgttacctaattcttcctagctactactac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctctc