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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCCGCAGGGGGCGCCGTGATGGGGAAGCCAGGCCCCGGGGTCGTTGACGCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcctccggtccctccgtctcgtcaaatttgctacttgctagcagtgctctgtgtcttatagtatcggatggtggctattgaaactattctctc...

Basic information

species Zea mays
transcript GRMZM2G133082_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133082_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g34180.1 (Oryza sativa), 5'ss of exon 1
---CCTCCGCAGGGGGCGCCGTGATGGGGAAGCCAGGCCCCGGGGTCGTTGACGCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcctccggtc-cctccgtctcgtcaaattt--gctacttgctagcagtgct-ctgtgt-cttatagtatcgg-atggtggctattgaaactattctctc
    | ||||    | ||| |||||||||||| | ||| ||| ||  |    ||||||||||||||||||||||||||||| |||||||||||| |||||||||| ||| ||| ||   | || ||| |||| ||| |||  | |  |||     | ||   | | || ||  | |  |||      | ||| | |||    |      
CCTTCGCCGCCACCGCCGCGGTGATGGGGAAGGCCGGCACCGCGGAAGC---CGCCGACGCCGGGATGGACGCCGTCCAGCAGCGGCTCATGTTCGAGGACGAgtaagtggccgccacccaccgccgcctcgccaacttttgggttgttgtggagattgtggcggcgtgctcgttgggtcgttgacttagctgtcgaattggt------

upper sequence: GRMZM2G133082_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G47770.1 (Glycine max), 5'ss of exon 1
-----CCTCCGCAGGGGGCGCCGTGATGGGGAAGCCAGGCCCCGGGGTCGTTGACGCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcctccggtccctccgtctcgtcaaatttgctacttgctagcagtgctctgtgtcttatagtatcggatggtggctattgaaactattctctc--
     ||| | |      | |||  |||||    | || |  | |       | ||| || ||||| ||||||||||||||||| || |||||||| || |||||||  ||| |   |  ||        |  |  ||||   ||  ||   | | |  |||   ||   |  | |  | |  ||  |   |    | ||   |   
CGCCTCCTTCTCCTCTCACACCGCCATGGG----CGAGACTTCCG--CTCCCGCCGCTGATGCCGGCATGGACGCCGTCCAGCGCCGTCTCATGTTCGAAGACGAGtccgttcctctccctcttcattcgtttttcaattacttatgtgtctg-attcttctaattcgcgttttctgtggttttgttttgcgtgtttgtttgtttgt

upper sequence: GRMZM2G133082_T03 (Zea mays), 5'ss of exon 1
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 5'ss of exon 1
CCTCCGCAGGGGGCGCCGTGATGGGGAAGCCAGGCC-CCGGGGTCGTTGACGCCG---ACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcctccggtcc----ctccgtctcgtcaaatttgctacttgctagcagtgctctgtgtcttatagtatcggatggtggctattgaaactattctctc--
     |  ||   | | ||  |     | ||   || |||   | | |||||| |   ||||||| |||||||| || ||||| || |||||||| ||||||||||||||  | |      |    |||  | ||||    ||||  |  || | | | ||||  |    | |  | | |   ||   |  | || |||| ||   |   
----GGAGGGCATCTCTGTCCTTTTCCACCCGCTCCACCGCCATGGGTGACGCTGTTGACGCCGGCATGGACGCTGTTCAGCGCCGCCTCATGTTCGAGGACGAgtgagtcacttttctctctgtactctctttcgttgtttttg--atctgtttgga-tgctgagaaaatcaaggaaac---tgaacgaaaatggaactttttggttgg

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|211304673|gb|FL135311.1|FL135311
EST:     GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttctatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
EST: gi|26557862|gb|CA830097.1|CA830097
EST:     GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttctatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
EST: gi|67022742|gb|CO451491.1|CO451491
EST:     GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttctatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
EST: gi|211304675|gb|FL135313.1|FL135313
EST:     GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttctatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
EST: gi|78120927|gb|DV539311.1|DV539311
EST:     CCCGACCCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttctatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
EST: gi|211036240|gb|FL120750.1|FL120750
EST:     CCGACGCCGGGATGGACGCCGTC-AGCGG-GGCTTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: CCGACGCCGGGATGGACGCCGTCCAGCGGCGGCT-CATGTTTGAGGACGAgtgagttgcc ... ttctatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
EST: gi|154130466|gb|EC872180.2|EC872180
EST:     GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttctatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
EST: gi|37421690|gb|CF648546.1|CF648546
EST:     GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttctatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
EST: gi|21843201|gb|BQ703782.1|BQ703782
EST:     GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttctatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
EST: gi|211304672|gb|FL135310.1|FL135310
EST:     GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGA                         GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA
genomic: GCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcc ... ttctatgcagGTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCCGCAGGGGGCGCCGTGATGGGGAAGCCAGGCCCCGGGGTCGTTGACGCCGACGCCGGGATGGACGCCGTCCAGCGGCGGCTCATGTTTGAGGACGAgtgagttgcctccggtccctccgtctcgtcaaatttgctacttgctagcagtgctctgtgtcttatagtatcggatggtggctattgaaactattctctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA