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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctgtttttcttgttttaaccttttgttattcctaccagtactgttgtaccattacattatgcatttaatacctgttcattatctttatgctta...

Basic information

species Zea mays
transcript GRMZM2G147884_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147884_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 5'ss of exon 10
TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagc-tgtttttcttgttttaaccttttgttattcctaccagtactgttgtaccattacattatgcatttaatacctgttcattatctttatgctta--
||||||||| || || ||||||||||| || || ||  | || ||||||||| ||||||||||||| ||||| |||||||||||||| || || ||||| |||||||| |  | ||   || | | || |||  ||||  | || ||  || |||||||| | |  | |  |  | |||||| ||||| | ||  | |||   
TAATGTGCACAACAACGCTTTCTATGCCGAGGAAAAACTACTGAAATCTGAGCTGCAAGCAATGCGAGATTGTGACCCTTCATCTGCACGGCATTGGATCgtaagagcatcatctttcagtatcatcccttttatattg-tgccggtgttgatgtaccatgata--acgtttccagtacctggtcattgttttctttcttcag

upper sequence: GRMZM2G147884_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA06G18810.1 (Glycine max), 5'ss of exon 9
TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctgttt---ttcttgttttaaccttttgttattcctaccagtactgttgtaccattacattatgcatttaatacctgttcattatctttatgctta
 ||||| || |||||||| ||||||||||||||||  ||||||| |||||| ||| |||| |||||||||||| |  |||   |||| || || ||| |||||||   | | |   || |      ||| |     ||||       ||| | ||| |   |  ||   ||  |  ||||| | ||    ||    ||| | |
GAATGTTCACAATAATGCATTCTATGCTGAAGAGACTTTGCTCAGATCTGAATTGGAAGCCATGCGTGATTGCAATTCTTTGACTGCTCGGCATTGGGTTgtaagtcttttgtgggttttaccgccaacttcaaactattggagttggtaattttgaattttgtcaaactg--tcgaatacttatttgc-attgcaatgatca

upper sequence: GRMZM2G147884_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA18G20800.1 (Glycine max), 5'ss of exon 9
TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctgtttttcttgttttaaccttttgttattcctaccagtac-tgttgtaccattacattatgcatttaa-tacctgttcattatctttatgctta-
 ||||| ||||| ||||| || ||||| || || ||  |||| ||||| || ||| |||||||||||||||| || |||| |||||| || |||||||||||||  | | ||  |  | ||  ||||   | ||      |  |  |  | ||     |||| ||| |     |   |   | ||  |  | |   ||   | 
-AATGTTCATAACAATGCATTTTATGCCGAGGAAAAACTGCTTAAATCAGAATTGGAAGCAATGCGTGATTGTGATCCTTTATCTGCTCGTCACTGGATTGtaa--gttcttactgattttgaaaccccctcttcccaggaaaaaaaaatattcagatattaaattttttgcctgggtgaatatttctgctgtcactgtccac

upper sequence: GRMZM2G147884_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G04360.1 (Glycine max), 5'ss of exon 9
TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctgtttttct---tgttttaaccttttgttattcctaccagtac---tgttgtaccattacattatgcatttaatacctgttcattatctttatgctta
|||||| || || ||||| || |||||||| || ||  |||| ||||| || | | ||||||||||||||||  |||||| |||||| || || |||||||||||  |  |     |   | || |||         ||  | |  || |       || | ||| |||  || |   |  | | ||   | ||| |  |      
TAATGTTCACAACAATGCATTTTATGCTGAGGAAAAACTGCTTAAATCAGAATCGGAAGCAATGCGTGATTGTAACCCTTTATCTGCTCGACATTGGATTgtaagttccttccacttgtatattataaaaaaaaaaaataacaaaaagaagaagcaatgaaacat-acaaaattccaatttttcttggcgaatatttccac-----

upper sequence: GRMZM2G147884_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA04G36130.1 (Glycine max), 5'ss of exon 4
TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctgtttt--tcttgtt-ttaaccttttgttattcctaccagtactgttgtaccattacattatgc-atttaatacctgttcattatctttatgctta
 ||||| || |||||||| ||||||||||||||||  ||||||| |||||| ||| |||| |||||||||||| |  |||   |||| || || ||| |||||||   | | |   ||||      ||| |     ||||  | |  ||| | |||   ||||   | | ||  || ||||| | ||    ||  | |  |   
GAATGTTCACAATAATGCATTCTATGCTGAAGAGACCTTGCTCAGATCTGAATTGGAAGCCATGCGTGATTGCAATTCTTTGACTGCTCGACATTGGGTTgtaagtcttttgtgggtcttacagccaacttcaaactattgatgctggtaattttg---cattttgtcaagctgttgaatacttatttgcaatgatcagacaa-

upper sequence: GRMZM2G147884_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA17G09290.1 (Glycine max), 5'ss of exon 9
TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctgtt---tttcttgttttaaccttttgttattcctaccagtactgttgtaccattacattatgcatttaatacctgt-------tcattatctttatgctta-----------------------------------------------------------------------------------
|||||| || |||||||| || |||||||||||||   ||||||||||||| ||| |||| |||||||||||| | ||||   |||| || || |||||||||||   ||     ||||| |     |  | ||  ||| | |   | || | |  |||  | | | |       || |  || |       |  ||   | | | ||||                                                                                   
TAATGTTCACAATAATGCATTTTATGCTGAAGAGACTCTGCTCAAATCTGAATTGGAAGCCATGCGTGATTGCAATCCTTTGGCTGCTCGACATTGGATTgtaaggcttgcccactttctagagccgaattcttactatccatgttaataatttcatactttgaaactgaattcatatttgctatggtgaaatagttgattatttccttacaatacaccgacaattatatctcaacatatttttttatttaattaattaaatgacaatggttaccatttcattgatgcttcag

upper sequence: GRMZM2G147884_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA01G03200.1 (Glycine max), 5'ss of exon 4
TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagc-tgtttttcttgtttta-accttttgttattcctaccagtactgttgtaccattacattatgcatttaatacctgttcattatctttatgctta
||||||  | || ||||| || ||||| || || ||  |||| ||||| || ||| ||||||||||||||||  |||||| |||||| || |||||||| |||||  | |     |  | | ||| |       | |     |  || |    || | |||  ||  || |   |  | | || | | ||| |  || |   
TAATGTTTACAACAATGCATTTTATGCAGAGGAAAAACTGCTTAAATCAGAATTGGAAGCAATGCGTGATTGTAACCCTTTATCTGCTCGACACTGGATCgtaagttcctaccacttgtatattataagaaaaataacaaaaagaagaagaaatgaaacat-gcaaaattccaatttttcttggtgactatttccatccac-

upper sequence: GRMZM2G147884_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G38990.1 (Glycine max), 5'ss of exon 9
TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctgtttttcttgttttaaccttttgttattcctaccagtactgttgtaccatta-cattatgcatttaatacctgttcattatctttatgctta-
|||||| ||||| ||||| || ||||||||||| ||  |||| ||||| ||  || |||||||||||||||| ||||||| |||||| || |||||||||||||  | | ||  |  | ||  ||||   | |       |  |  | | ||     ||||   || | |  |   |   | ||  |  | |   ||   | 
TAATGTTCATAACAATGCATTTTATGCTGAAGAAAAACTGCTTAAATCAGAAATGGAAGCAATGCGTGATTGTGACCCTTTATCTGCTCGTCACTGGATTgtaa--gttcttactgattttgaaaccccctctccccaggaaaaaaaatattcagatattaatttttttccctgggtgaatatttctgctgtcactgtccac

upper sequence: GRMZM2G147884_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 5'ss of exon 9
TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagag-ctgtttttcttg---ttttaaccttttgttattcctaccagtactgttgtaccattacattatgcatttaatacctgttcattatctttatgctta
|||||| ||||| ||||| |||||||||||||||||  |||| |  |||||  |||||||||||||||||||| | |||| ||||||||| ||||||||||||||   |  | | |  |    ||||  | ||   || |  || ||    |      | |    |    | |  | ||  | | || |  |     | ||   
TAATGTTCATAACAATGCATTCTATGCTGAAGAGAAACTGCTTAGGTCTGAAATGCAAGCAATGCGTGATTGCAATCCTTTATCTGCCCGACACTGGATTgtaagtttccatatcttatagaattttttctttccattctctctcccctcccaaccccaaccactcccactcctctgaaggcatattta--actgacaagca--

upper sequence: GRMZM2G147884_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv17s0000g09100.t01 (Vitis vinifera), 5'ss of exon 9
TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctgtttttcttgttttaaccttttgttattcctaccagtactgttgtaccattacattatgcatttaatacctgttcattatctttatgctta---
||||||||| |||||||| || ||||||||||| ||  |||||| ||||||  ||||||| ||||||||||| || || |  ||||||||||| |||||||||||   |  ||  | || ||  |   ||| | |     | |  || | |  |    ||  || |    |||  |   ||  | |    |  ||||||    
TAATGTGCACAATAATGCATTTTATGCTGAAGAAAAACTGCTCAGATCTGAAATGCAAGCTATGCGTGATTGTGATCCATTGTCTGCCCGCCATTGGATTgtaagtcatccttgccctgcttctataatttataaaatggatctatattttgttttgtttgtatcacatgttttgtgagtgggcttg---taaatgcttgcaa

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|32919574|gb|CF024386.1|CF024386
EST:     AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATT                         GTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
genomic: AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctg ... ttcctttcagGTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
EST: gi|211381837|gb|FL377365.1|FL377365
EST:     AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATT                         GTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
genomic: AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctg ... ttcctttcagGTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
EST: gi|211506668|gb|FL391689.1|FL391689
EST:     AGTTGCAAGCAATGCGTGATTGCNACCCTTCATCTGCCCGCCACTGGATT                         GTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
genomic: AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctg ... ttcctttcagGTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
EST: gi|211134086|gb|FL422141.1|FL422141
EST:     AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATT                         GTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
genomic: AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctg ... ttcctttcagGTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
EST: gi|50326819|gb|CO521945.1|CO521945
EST:     AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATT                         GTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
genomic: AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctg ... ttcctttcagGTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
EST: gi|60342955|gb|DN209928.1|DN209928
EST:     AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATT                         GTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
genomic: AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctg ... ttcctttcagGTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
EST: gi|67025362|gb|CO454111.1|CO454111
EST:     AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATT                         GTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
genomic: AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctg ... ttcctttcagGTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
EST: gi|60353904|gb|DN220877.1|DN220877
EST:     AATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATT                         GTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
genomic: AATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctg ... ttcctttcagGTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
EST: gi|50326829|gb|CO521955.1|CO521955
EST:     AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATT                         GTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
genomic: AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctg ... ttcctttcagGTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
EST: gi|211466963|gb|FL423374.1|FL423374
EST:     AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATT                         GTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
genomic: AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctg ... ttcctttcagGTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
EST: gi|31348944|gb|CD433301.1|CD433301
EST:     AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATT                         GTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
genomic: AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctg ... ttcctttcagGTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
EST: gi|21621426|gb|BQ619432.1|BQ619432
EST:     AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATT                         GTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
genomic: AGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctg ... ttcctttcagGTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
EST: gi|78022408|gb|DV490795.1|DV490795
EST:     TTCATCTGCCCGCCACTGGATT                         GTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG
genomic: TTCATCTGCCCGCCACTGGATTgtaagagctg ... ttcctttcagGTACGCAACACACGAACTGTGAATCGGACGGGGCAGCCAACTGGCTACAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAGCAATGCGTGATTGCGACCCTTCATCTGCCCGCCACTGGATTgtaagagctgtttttcttgttttaaccttttgttattcctaccagtactgttgtaccattacattatgcatttaatacctgttcattatctttatgctta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA