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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATCTGCCGGTTGGTGGATATACTGATCTGTTTGTCCGCTGCAGGTCATTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaatcttcagacctggccagctgaatactgttttaccataccgatagatgttcaatctgttaatactgatcgtgcaattattacttgtcttggtag

Basic information

species Zea mays
transcript GRMZM2G073535_T05
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073535_T05 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g41900.3 (Oryza sativa), 5'ss of exon 3
GGTATCTGCCGGTTGGTGGATATACTGAT----CTGTTTGTCCGCTGCAGGTCATTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaatcttcagacctggccagctgaatactgttttacca-taccgata-gatgttcaatctgttaatactgatcgtgcaattattacttgtcttggtag
    | | | | |  | |||| | ||| |        ||    | |||||||||||||||| |||||||| ||||| ||||||||||| || ||||||||||||||||| |||||  ||||| | |  |       |        |  | | | | || | ||  | || | |  || ||||   ||   || |  ||  | ||| |||
----TTTTCTGCTATGAGGATGTGCTGGTAACGTAAATTTGTGGTTGCAGGTCATTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAGgtattgagaattatcagagcagagctatgacttctcaagagattaatgctgctaagttgacctatttat--attctgaatctgattttttatctctttttgctag

upper sequence: GRMZM2G073535_T05 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g41900.2 (Oryza sativa), 5'ss of exon 3
GGTATCTGCCGGTTGGTGGATATACTGATCTGTTTGTCCGCTGCAGGTCATTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaatcttcagacctggccagctgaatactgttttacca-taccgata-gatgttcaatctgttaatactgatcgtgcaattattacttgtcttggtag
                                              ||||||||||| |||||||| ||||| ||||||||||| || ||||||||||||||||| |||||  ||||| | |  |       |        |  | | | | || | ||  | || | |  || ||||   ||   || |  ||  | ||| |||
----------------------------------------------GTCATTCAGCTTCAAGGTGATCAGCGTAAGAATGTTGCCACGTTCCTAGTTCAGgtattgagaattatcagagcagagctatgacttctcaagagattaatgctgctaagttgacctatttat--attctgaatctgattttttatctctttttgctag

upper sequence: GRMZM2G073535_T05 (Zea mays), 5'ss of exon 3
lower sequence: EDP05192 (Chlamydomonas reinhardtii), 5'ss of exon 2
GGTATCTGCCGGTTGGTGGATATACTGATCTGTTTGTCCGCTGCAGGTCATTCAGCTCCAAGGTGACCAGCGCAAGAATGTT-GCTACTTTC--CTAGTTCAGgtattc----agaatcttcagacct-ggccagctgaatactgttttaccataccgatagatgttcaatctgttaatactgatcgtgcaattattacttgtcttggtag------------------------------------------------------------------
                                     | |    ||||||||||||| || || |||||||||||||||||  || |||| |  || |  |||    ||    ||||    |||| |  ||   |       | | |      |||  |   || |||| | | | |||   ||| | || |    ||    |   |   |                                                                  
------------------------------CCCGGAGCTGGGCAAGGTCATTCAGCTGCAGGGCGACCAGCGCAAGAATGTCAGCGACTTCCTGCTGGGCCAGAAGCTCGTGAAGAAGGACCAGATCAAGgttcgtccgggtcgggtcgggactacatacgaat-ttcagt-tctaaatctcgattgcgctagcgctagcccttcggagcgcgggccgcaccttttaacagccctaacactatggtggtgctacccttgcccccctgcaacccacag

upper sequence: GRMZM2G073535_T05 (Zea mays), 5'ss of exon 3
lower sequence: PP1S23_225V6.1 (Physcomitrella patens), 5'ss of exon 2
GGTAT-CTGCCGGTTGGTGGATATACTGATCTGTTTGTCCGCTGCAGGTCATTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaatcttcagacctggccagctgaatactgttttaccataccgatagatgttcaatctgttaatactgatcgtgcaattattacttgtcttggtag-
| | | ||||      ||||   | | |  |     ||  | | |||||||||||||| || ||||||||||| ||||||||  | |  || || || |||||| |    |  |  |   ||| |  ||  ||| |           |   ||  | |||   | | | | |    |   |        ||| ||   || |   
GTTTTGCTGCAACGGAGTGGTGGTGCAGGACCCAGAGTTGGGT-CAGGTCATTCAGCTGCAGGGTGACCAGCGGAAGAATGTCTCCAACTTTCTCGTCCAGgtacttgtcactt--atgactgccttgc--aatgcgtcacggtttgaagcatgcacgtttggtatttaactgtaaagaatatgtcacctacctgatgtgctcca

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|32847379|gb|CD987060.1|CD987060
EST:     TTCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|211398054|gb|FL283736.1|FL283736
EST:     TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATYAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|161407609|gb|DW042454.1|DW042454
EST:     TACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGCTCTAAGGGACC
genomic: TACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|15215361|gb|BI431254.1|BI431254
EST:     TGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|33095396|gb|CF055390.1|CF055390
EST:     TTCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|32945511|gb|CF050330.1|CF050330
EST:     TTCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|56462076|gb|CK986374.1|CK986374
EST:     TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|32848742|gb|CD988423.1|CD988423
EST:     TCCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|32847457|gb|CD987138.1|CD987138
EST:     TTCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGAGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|71596289|gb|DR907040.1|DR907040
EST:     TTCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|87153805|gb|DY398594.1|DY398594
EST:     TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|32930505|gb|CF035317.1|CF035317
EST:     TTCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|32857359|gb|CD997040.1|CD997040
EST:     AGCGCAAGAATGTTGCTACTTTCCTAGTTCGG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAGGGGACC
genomic: AGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|19351098|gb|BM895630.1|BM895630
EST:     TTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|31352015|gb|CD436372.1|CD436372
EST:     GCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: GCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|19436191|gb|BM952601.1|BM952601
EST:     TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|32928360|gb|CF033172.1|CF033172
EST:     TTCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|5361088|gb|AI795703.1|AI795703
EST:     TTCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|84980515|gb|DW530864.1|DW530864
EST:     GCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: GCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|29130959|gb|CB381663.1|CB381663
EST:     CGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: CGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|116826024|gb|EC869774.1|EC869774
EST:     GCTA-TTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: GCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|32846881|gb|CD986562.1|CD986562
EST:     TTCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|32846459|gb|CD986140.1|CD986140
EST:     TTCAGCTCCAAGGCGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|32847710|gb|CD987391.1|CD987391
EST:     TTCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|113630309|gb|DW788252.1|DW788252
EST:     TACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|18172656|gb|BM348044.1|BM348044
EST:     TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|33097538|gb|CF057498.1|CF057498
EST:     TTCAGCTCCAAGGTGATCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|211191718|gb|FL380854.1|FL380854
EST:     TTCAGCTCCAAGGTGATCAGCGCAMGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: TTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
EST: gi|32850202|gb|CD989883.1|CD989883
EST:     CGCAAGAATGTTGCTACTTTCCTAGTTCAG                         GCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC
genomic: CGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaa ... gtcttggtagGCTGGGATTGCGAAGAAAGAGAACATCAAGATTCACGGGTTCTAAGGGACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTATCTGCCGGTTGGTGGATATACTGATCTGTTTGTCCGCTGCAGGTCATTCAGCTCCAAGGTGACCAGCGCAAGAATGTTGCTACTTTCCTAGTTCAGgtattcagaatcttcagacctggccagctgaatactgttttaccataccgatagatgttcaatctgttaatactgatcgtgcaattattacttgtcttggtag

- - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA