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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTCTCTTGGTGATGCAAGGGCATATTACCTTTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagggtgcaaaatgcaatttgtttacatggaactgctatcgttattctagattttgttaatgttgcttcccacatgtttcctcag

Basic information

species Zea mays
transcript GRMZM5G841900_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G841900_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g57070.2 (Oryza sativa), 5'ss of exon 4
------------------CTTTCTCTTGGTGATGCAAGGGCATATTACCTTTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatg------------------------------------------------gaagggtgcaaaatgcaatttgtttacatggaactgctatcgttattctagattttgtt----aatgttgcttcccacatgtttcctcag
                  || ||||||||||||||||||||||||||||||||||||||  | |||||||| ||||| ||||| |||||||| ||| |||||| |                                                ||||| | ||  ||||||| ||| |   || ||  | |    || |||    |  ||||    ||||| ||| |     |||| |  |||
CCTTAAATCATCTTAAAGCTCTCTCTTGGTGATGCAAGGGCATATTACCTTTCCACTGCCCAGAATGAACTCGGAGTTGTTTCTGCACAAAGTATAACTGgtaggtgttttctaatattggagtgccaaattactcactattgatttttagctgaaggatacatcatgcaatgtgtgtgtgtgaaatagtttcaattgttcccagtagtgttctgtaatgtggctgctt-tgtgttgctccag

upper sequence: GRMZM5G841900_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g57070.1 (Oryza sativa), 5'ss of exon 5
CTTTCTCTTGGTGATGCAAGGGCATATTACCTTTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatg------------------------------------------------gaagggtgcaaaatgcaatttgtttacatggaactgctatcgttattc----tagattttgttaatgttgcttcccacatgtttcctcag
|| ||||||||||||||||||||||||||||||||||||||  | |||||||| ||||| ||||| |||||||| ||| |||||| |                                                ||||| | ||  ||||||| ||| |   || ||  | |    || |||    |||  ||   |||||| ||| |     |||| |  |||
CTCTCTCTTGGTGATGCAAGGGCATATTACCTTTCCACTGCCCAGAATGAACTCGGAGTTGTTTCTGCACAAAGTATAACTGgtaggtgttttctaatattggagtgccaaattactcactattgatttttagctgaaggatacatcatgcaatgtgtgtgtgtgaaatagtttcaattgttcccagtagtgttctgtaatgtggctgctt-tgtgttgctccag

upper sequence: GRMZM5G841900_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA20G36410.1 (Glycine max), 5'ss of exon 6
CTTTCTCTTGGTGATGCAAGGGCATATTACCTTTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagggtgcaaaatgcaatttgtttacatggaactgctatcgttattctagattttgttaat-gttgcttcccacatgtttcc-tcag---------
||||||||||| |||||| ||||||| |  || || ||||| || ||||||||||| || ||||| ||| ||||||| ||||||  |     |   | | |        |  ||    |   |   | ||  || |||  ||||||  | ||| | ||    |||||    | ||         
CTTTCTCTTGGAGATGCACGGGCATACTTTCTATCTACTGCAAAGAATGAACTTGGTGTTGTTTCTGCAGAAAGCATTGCTGgtgagattttgctaatattctgggagttaaacccttataagtggttgtggttgtag--tttgttgctagttccctctagtatgttaatgttagtgacttacg

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|148935198|gb|EC879233.2|EC879233
EST:     TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
EST: gi|60336704|gb|DN203677.1|DN203677
EST:     TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
EST: gi|211102907|gb|FK962288.1|FK962288
EST:     TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACC
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACC
EST: gi|148991615|gb|EE033149.2|EE033149
EST:     TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
EST: gi|78180011|gb|DV550384.1|DV550384
EST:     TTCCACTACGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
EST: gi|12046009|gb|BF728044.1|BF728044
EST:     TTCCACTACGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
EST: gi|211326704|gb|FL445906.1|FL445906
EST:     TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
EST: gi|60341943|gb|DN208916.1|DN208916
EST:     TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
EST: gi|28873659|gb|CB329617.1|CB329617
EST:     TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
EST: gi|148965500|gb|EE016317.2|EE016317
EST:     TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
EST: gi|18180077|gb|BM381287.1|BM381287
EST:     TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
EST: gi|71439027|gb|DR820077.1|DR820077
EST:     TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
EST: gi|71759867|gb|DR957804.1|DR957804
EST:     TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
EST: gi|148935199|gb|EC879234.2|EC879234
EST:     TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTG                         GTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG
genomic: TTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagg ... gtttcctcagGTGGTACATTGGTTCCAATCAGTTGGACTGAGATGCAATGTGATTTGACCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTCTCTTGGTGATGCAAGGGCATATTACCTTTCCACTGCGAAAAATGAACTTGGAGTCGTTTCAGCACAAAGCATAGCTGgtatggaagggtgcaaaatgcaatttgtttacatggaactgctatcgttattctagattttgttaatgttgcttcccacatgtttcctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG