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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtctgtcgtctgctagaccatcaggctactacggctgcttgagatctgtgtggtcatgctaaatttcatcattcagtagtttagtcgatgtctgaataaagatgtgttttctgtatgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG

Basic information

species Zea mays
transcript GRMZM2G087192_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087192_T02 (Zea mays), 3'ss of exon 2
lower sequence: 13113.m00235 (Oryza sativa), 3'ss of exon 3
gtacgtctgtcgtctgctagaccatcaggctactacggctgcttgagatctgtgtggtcatgctaaatttcatcattcagtagtttagtcgatgtctgaataaagatgtgttttctgtatgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG
    ||||||    | |||||   | |||||     | ||   ||| || |     | |||| | |||| | |  ||     ||| |  | || | | || |   |  ||||| ||||||||   |||||||||| || |||||||| ||||||||  | |||||||| ||||| |||||||| ||||||||||| |||||    |||||||| |||||||||||||||
----gtctgta---tcctagattgttaggctgt---gactttctgaaatttcatgagccatgttcaattgcct--tttgacggttcaa-caatctttaaagatcaa-atgtttcctgtatgcatgcaagGTACAAAGATACTCCTGGTATTTGGACAAAGGAGCAAGTGGAAGCGTGGAAGCCAATCGTAGACGGCGTTCATGCCAAAGGAGGAATATTTTTCTGTCAG

upper sequence: GRMZM2G087192_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ25413 (Selaginella moellendorffii), 3'ss of exon 2
gtacgtctgtcgtctgctagaccatcaggctactacggctgcttgagatctgtgtggtcatgctaaatttcatcattcagtagtttagtcgatgtctgaataaagatgtgttttctgtatgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG
                                                   |||    | || |   ||||  |||||  | ||||    ||  |      ||   ||  |||    ||| |||| |               ||||| || ||| |  | |||||||||||||||||||||||||| ||  | |  |||||  | |||||||   | || ||    |||
---------------------------------------------------gtgaaagc-tgttc--tttctccattctcttgttttactgaact----gcaagcttggatttcagATATCCGCATAG-------------CCCTGGAATCTGGTCAGAGGAGCAAGTCGAAGCATGGAAGCCGATTGTCCAGGCTGTTCATGACAAAGGAGCTGTTTTCTTTCTACAG
















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|211046904|gb|FL342230.1|FL342230
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211459461|gb|FL315095.1|FL315095
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211438615|gb|FL361924.1|FL361924
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|78105288|gb|DV523706.1|DV523706
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCAT
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCAT
EST: gi|211049230|gb|FL320166.1|FL320166
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211372990|gb|FL342986.1|FL342986
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211086396|gb|FL335516.1|FL335516
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211004021|gb|FL317949.1|FL317949
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211538244|gb|FL353979.1|FL353979
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211516970|gb|FL321888.1|FL321888
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCAT
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCAT
EST: gi|91878868|gb|EB408825.1|EB408825
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|78113505|gb|DV531896.1|DV531896
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAA
EST: gi|211399636|gb|FL347340.1|FL347340
EST:     GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGG                         GTACAAGGACACTCCTGGCATTTGGACC-ATGAGCAAGTCGAAGCATGG
genomic: GGAGGTCTTCTGATCGCTGAGGCCACGGGGGTTTCAGACACTGCTCAAGGgtacgtctgt ... tgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcagtagtttagtcgatgtctgaataaagatgtgttttctgtatgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG
                        aataaagat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtctgtcgtctgctagaccatcaggctactacggctgcttgagatctgtgtggtcatgctaaatttcatcattcagtagtttagtcgatgtctgaataaagatgtgttttctgtatgcgcacaagGTACAAGGACACTCCTGGCATTTGGACCCATGAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG