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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCAACAGCATTCTCGTCGTCACCATCAACGGCATCGGCCTCGTCATCGAGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcgtgccatgttgttcgcccgatccatgatctgtccctgctgttgtttccctccacgtgtagtgtatctctcatctggtggtggtttttgagcttaatgcag

Basic information

species Zea mays
transcript GRMZM2G157675_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157675_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g08030.1 (Oryza sativa), 5'ss of exon 1
------CCCCAACAGCAT---TCTCGTCGTCACCATCAACGGCATCGGCCTCGTCATCGAGGCCGTCTAC-CTCACTATC--TTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtg--tcgtgccatgttgttc-gcccga-tccatgatctgtccctgctgttgtttccc-----tccacgt--gtagtgtatctctcatc-tggtggtggtttttgagcttaatgcag------------------------------------------
      || ||||    |     |||||| || | ||| |  | | |||||| || ||  | | |||  | |   ||  |   || ||    ||    ||    || |   |  ||  |   ||| ||  |     | || | | |  ||| ||||   ||  |   || ||||     |||||      ||  |     || ||    |    |   |||  |||      |                                          
CATGATCCGCAACGTGGTGGGCATCGTCGGCAACGTCATCTCCTTTGGCCTCTTCCTCTCGCCGGTCCCCACCTTCTGGCAAATCATCAAGAATAAGAACgtataggacttcaagacagacccgtacctggccacactgctcaactgtatgctctgggacttttacggtctccccatcgtccaccccaacagcatcctcgtcgtcaccatcaacggcattggccttgtcatcgagacctgtctatctcaccatcttcttcctcttctccgacaag

upper sequence: GRMZM2G157675_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g42110.1 (Oryza sativa), 5'ss of exon 2
CCCCAACAGCATTCTCGTCGTCACCATCAACGGCATCGGCCTCGTCATCGAGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagt--gtcgtgccatg--ttgttcgcccgatccatgatctgtccctgctgttgtttccctccacgtgtagtgtatctctcatctggtggtggtttttgagcttaatgcag
||||||||| || |||||||||||||||||||||||||||||| || |||||| |  |||||||   |||||||||||||| |||  || | |||| |||||  ||   |||  |||||   |||||      ||| |  ||  ||  | |  |  | |   ||    | || | || | |  | |   || |  | |    | |   |||||
CCCCAACAGTATCCTCGTCGTCACCATCAACGGCATCGGCCTCCTCGTCGAGGGCACCTACCTCCTCATCTTCTTCCTCTACTCCCCCAACAAGAAACGCgtacgtcgatcgatccatgatctgttcattatttccttcctcgatctatacattaatctttatcatgatctaat-taacccgtacc-attgatcatatcatcgatcg-tgcag

upper sequence: GRMZM2G157675_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g42090.1 (Oryza sativa), 5'ss of exon 2
CCCCAACAGCATTCTCGTCGTCACCATCAACGGCATCGGCCTCGTCATCGAGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagt--gtcgtgccatgttgttcgcccgatccatg-atctgtccctgctgttgtttccctccacgtgt-agtgtatctctcatctggtggtggtttttgagc-ttaatgcag
||| |||||||| |||||||||||||||||||||||||| ||| |  |||||| |  |||||||   |||||||||||||| |||  || | ||||||||||   |  |   | || |     | |    ||| ||  |||  |   | ||    ||    || |  | | | | |||||   || |  |  ||   ||    | ||  |||||
CCCGAACAGCATCCTCGTCGTCACCATCAACGGCATCGGTCTCATTGTCGAGGGCACCTACCTCTTCATCTTCTTCCTCTACTCCCCCAACAAGAAGCGCgtatatacgcttttccctccctcttgatatatctatatatccatatttcctcgatttaatttcgaaatttgaatctatctgaaatataatcttgacattaattcattgttgcag

upper sequence: GRMZM2G157675_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ26801 (Selaginella moellendorffii), 5'ss of exon 2
CCCCAACAGCATTCTCGTCGTCACCATCAACGGCATCGGCCTCGTCATCGAGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcgtgccatgttgttcgcccgatccatgatctgtccctgctgttgtttccctccacgtgtagtgtatctctcatct-ggtggtggtttttgagcttaatgcag
 || |||||| ||||||||||||||||||| |||||||||   |   |||||  |  ||||||     ||| |||  | ||  |    |   ||  | | |||||   ||       || | | |  | ||  | | || | |||    ||||||  ||   | |   |  |   |  |   | ||| |  ||||   ||          
TCCAAACAGCCTTCTCGTCGTCACCATCAATGGCATCGGCACTGCTCTCGAGAGCACCTACCTGTGCGTCTACTTGTTTTACGCTCCAAATAAGCCGAGAgtgagctacgctaatccttttgctcaagctctctcagcttttcctcaatttgtttttcttttccttctggtttcgtgacgcttcggttgctgtttgacag----------

upper sequence: GRMZM2G157675_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ26493 (Selaginella moellendorffii), 5'ss of exon 2
CCCCAACAGCATTCTCGTCGTCACCATCAACGGCATCGGCCTCGTCATCGAGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcgtgccatgttgttcgcccgatccatgatctgtccctgctgttgtttccctccacgtgtagtgtatctctcatct-ggtggtggtttttgagcttaatgcag
 || |||||| ||||||||||||||||||| |||||||||   |   |||||  |  ||| ||     ||| |||  | ||  |    |   ||  | | || ||   ||       || | | |  | ||  | | || | |||    ||||||| ||   | |   |  |   |  |   | | | |  ||||   ||          
TCCAAACAGCCTTCTCGTCGTCACCATCAATGGCATCGGCACTGCTCTCGAGAGCACCTATCTGTGCGTCTACTTGTTTTACGCTCCAAATAAGCCGAGAgtaagctacgctaatccttttgctcaagctctctcagcttttcctcaatttgtttctcttttccttctggtttcgtgacgcttcgattgctgtttgacag----------

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|211344463|gb|FL201420.1|FL201420
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGCTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|31628388|gb|CD526584.1|CD526584
EST:     AGGGCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCANAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|28188031|gb|CB179641.1|CB179641
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|211342073|gb|FL201410.1|FL201410
EST:     AGGST-TCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|31627932|gb|CD526360.1|CD526360
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|28188247|gb|CB179857.1|CB179857
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|211344467|gb|FL201424.1|FL201424
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCC
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCC
EST: gi|211342078|gb|FL201415.1|FL201415
EST:     AGGC--TCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|211342077|gb|FL201414.1|FL201414
EST:     GGCS-TGCTACCTCACTATCTTCTTCCTCTATTCCGRCAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCT
genomic: GGCCGT-CTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCT
EST: gi|37361336|gb|CF602625.1|CF602625
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|211344465|gb|FL201422.1|FL201422
EST:     GGCT-TCTTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGCTCGCCGTG
genomic: GGCCGTCT-ACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|211162572|gb|FL132731.1|FL132731
EST:     TATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGCTCGCCGTG
genomic: TATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|211342079|gb|FL201416.1|FL201416
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGGCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|148934526|gb|EC878568.2|EC878568
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|31628107|gb|CD526445.1|CD526445
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|14245092|gb|BG873674.1|BG873674
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|211344464|gb|FL201421.1|FL201421
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGT
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGT
EST: gi|211342075|gb|FL201412.1|FL201412
EST:     AGGCS-TCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGT
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCC-TGGCCGTGGAGATTCTGTTCATGGTCGCCGT
EST: gi|71317142|gb|DR795259.1|DR795259
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|211344466|gb|FL201423.1|FL201423
EST:     AGGC-GTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|28187755|gb|CB179365.1|CB179365
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTTCGCGATCCTGGCCGTGGAGATTCTTGTTCATGGTCGCCG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTT-CGCGATCCTGGCCGTGGAGATTCT-GTTCATGGTCGCCG
EST: gi|7138105|gb|AW499432.1|AW499432
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGGTCATGCTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|28188001|gb|CB179611.1|CB179611
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGTGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|24462465|gb|BM659996.1|BM659996
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|28187611|gb|CB179221.1|CB179221
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCAACAGCATTCTCGTCGTCACCATCAACGGCATCGGCCTCGTCATCGAGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcgtgccatgttgttcgcccgatccatgatctgtccctgctgttgtttccctccacgtgtagtgtatctctcatctggtggtggtttttgagcttaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC