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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttctgaaatgctgtgaatgctcctactcgtgccctaagtttagtcagtactatgcaaggtctcatggaagtataaaacgaaattcactttcatttcctattacag

Basic information

species Zea mays
transcript GRMZM2G118316_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118316_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os12g07060.1 (Oryza sativa), 5'ss of exon 13
----TGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttctgaaatgctgtg--aatgctcctactcgtgccctaagtttagtcagtactatgcaaggtctcatggaagtataaaacgaaattcactttcattt-cctattacag
     || || |||||||  |||||||||||||| |||||||||||||||||||| || ||||| |||||||| || |||||||||||||||||||  || ||    |  | |   ||    |  |||| |    | |||||  ||||| || |||||                   | ||| ||    ||||||| |||| |||||
GCATCGATGACAATGACACTATGAAGGTTTTTGGCAAGGGTGGTGCAGATGTTGAGCGCAATAAACCTGGTGATCTCTATGTTACTATCAAGgtttggttccttttttttttttccaaaatacaaactctttatgtcagtttgatcagttctttgcaa-------------------atgaactttgtattcattttcctagtacag

upper sequence: GRMZM2G118316_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA09G00580.1 (Glycine max), 5'ss of exon 13
----TGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgt---ttaatttctgaaatgctgtgaatgctcctactcgtgccctaagtttagtcagtactat--gcaaggtctcatggaagtataaaacgaaattcactttcatttcctattacag
     |||   || || | ||| ||||||| | | |  ||||| ||||||  |||  || || | |||||||| ||||||||||||||||||||   | |||  ||   | |  |  | |  |  |  |  | |  | |   | | || |  |||  |   |  ||  | | ||                                   
GGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAGgtacttcaatagcttggaagtcgcta-tttttttgttgatacttttaaacttgacatttttatttgtttgtcctttttgcag-----------------------------------

upper sequence: GRMZM2G118316_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA12G36820.1 (Glycine max), 5'ss of exon 13
----TGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttctgaaatgctgtgaatgctcctactcgtgccctaagtttagtcagtactatgcaaggtctcatggaagtataaaacgaaattcactttcatttcctattacag
     |||   || || | ||| ||||||||| | |  ||||| ||||||  |||  || || | |||||||| ||||||||||||||||||||   | |||   |||    ||   | |   | ||      |   ||| || | |||| |     ||||  ||  | | | |   |    ||  |||               
GGATAGACAGCAACGAGACCATAAAGGTTTTTAGAAGTGGTGGAGCAGATCCTGATGGAGATCACCCTGGTGATCTTTATGTTACTATCAAGgt---acttc---aatagcttgggagttggaagtctctattt---ttttgttaatactttt---agtct--tgacatttttatttgtttctcctttttgcag----------

upper sequence: GRMZM2G118316_T02 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA15G42640.1 (Glycine max), 5'ss of exon 13
----TGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttctgaaatgctgtgaatgctcctactcgtgccctaagtttagtcagtactatgcaaggtctcatggaagtataaaacgaaattcactttcatttcctattacag--
    |||| | ||||| |  || ||||||| | | |  ||||||||||||  |||  || |||| |||||||| ||||||||||||||||||||  || | || ||    |   |   || |    | ||       ||   |   || | |  |   ||||||  |||   |  |  |  ||   | |||||| |  ||      
GGATTGACAACAATGAAACTATAAAGGTTTATAGAAGTGGTGGTGCAGATCCTGATGGAGATAATCCTGGTGATCTTTATGTTACTATCAAGgt--aactcctcaataatttcaatctcttcatagcttggtgatcattccatttttattgtatatcttctcat--aagccca--atcattttttttatcattttcctttgtgcag

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|148947432|gb|EC892855.2|EC892855
EST:     GTGCAGATGTTGCCCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|71757144|gb|DR955081.1|DR955081
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|71769071|gb|DR967008.1|DR967008
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|17929416|gb|BM266376.1|BM266376
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|211267317|gb|FL091731.1|FL091731
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|93017255|gb|EB642775.1|EB642775
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|71427930|gb|DR808980.1|DR808980
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|18165643|gb|BM335482.1|BM335482
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAT                         GT-ATTTAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|60397506|gb|DN230322.1|DN230322
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|149101261|gb|EE187373.2|EE187373
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|6022509|gb|AW067542.1|AW067542
EST:     CCGAACTAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: CCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|60398827|gb|DN231643.1|DN231643
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|211267316|gb|FL091730.1|FL091730
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
EST: gi|86469547|gb|DY235917.1|DY235917
EST:     GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAG                         GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT
genomic: GTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttc ... cctattacagGTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgtttaatttctgaaatgctgtgaatgctcctactcgtgccctaagtttagtcagtactatgcaaggtctcatggaagtataaaacgaaattcactttcatttcctattacag

- - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - -  CAGATG