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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgcaacaactcctgacttagatatgttttattatgcagctatctgtggtattgctatcccggactagcagttttcatgttttaggtctttcatagcttgtgtgccaaggtcctttttgtaatcagatgcatctcctaatttgcaatgccatttgacctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAAGACAAGCGTTACAAGAACCGCGAACTGCAGACCATGCGCCTCCTTGACC

Basic information

species Zea mays
transcript GRMZM5G835235_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835235_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 4
gttagttgcaacaactcctgacttagatatgttttat---------------tatgcagctatctgtggtattgctatcccggactagcagttttcatgttttaggtctttcatagct--tgtgtgccaaggtcctttttgtaa------tcagatg-----catctcctaatttgcaatgccatttgacctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAAGACAAGCGTTACAAGAACCGCGAACTGCAGACCATGCGCCTCCTTGACC
||||||||||||| ||   |  ||  |||| ||| |                || | ||||| || |   ||   || | |  |||||||    |  | || || ||     || | |  |    |  ||  | || ||  |||        | |||     ||| ||   | | |  ||  |||||   |  ||   |||| || ||| |||| || |||||||| ||||| || |||||||||||||| || ||||| ||||||||||| || || |||||||||||||| |||||||
gttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaact-taacatcattaactct-actagcaccactttttttgtatgtagcaaattgttgatacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAGGATAAGCGCTACAAGAACCGTGAGCTTCAGACCATGCGCCTTCTTGACC

upper sequence: GRMZM5G835235_T04 (Zea mays), 3'ss of exon 4
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagttgcaacaactcctgacttagatatgttttattatgcagctatctgtggtattgctatcccggactagcagttttcatgttttaggtctttcatagcttgtgtgccaaggtcctttttgtaatcagatgcatctcctaatttgcaatgccatttgacctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAAGACAAGCGTTACAAGAACCGCGAACTGCAGACCATGCGCCTCCTTGACC
                                                            || |    ||| |       ||||     | ||| ||  |  |   ||  ||||||  |      ||  ||  | || | || ||    |  |  ||||    ||||   |||| || ||  | || |  || || ||||| || || |||||||| ||||| |||||| | ||||||||||| ||||| |||| |||||| || || || |
------------------------------------------------------------taacttc-actggagccagacatggggctgatctgtc-catgtgacgt-tcaaggtggt----agaactagg-ggatgttctgatcgcgagggtaattt----tgttgtcagGCAAAATGCATAGAGAGCGGAGAAACTGTGGCTATTAAGAAGGTGCTTCAGGACAAGAGATACAAGAACCGAGAACTTCAGATCATGCGGCTGCTGGAGC

upper sequence: GRMZM5G835235_T04 (Zea mays), 3'ss of exon 4
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 4
gttagttgcaacaactcctgacttagatatgttttattatgcagctatctgtggtattgctatcccggactagcagttttcatgttttaggtctttcatagcttgtgtgccaaggtcctttttgta-atcagatgcatctcctaatttgcaatgccatttgacctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAAGACAAGCGTTACAAGAACCGCGAACTGCAGACCATGCGCCTCCTTGACC
                                                                                                        || |  | || |||     ||  | || | |||     ||   |    |     |      |     |||||||||| |||||||| || || || || || || || ||||| || ||||||||||| ||||||||||| || || ||||  ||||||||||| ||||
--------------------------------------------------------------------------------------------------------gtattgctag-tccaaacagtgcaacaaaagcaggctttatcgtttcttctttctctttgggaatgcagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGGTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

upper sequence: GRMZM5G835235_T04 (Zea mays), 3'ss of exon 4
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 4
gttagttgcaacaactcctgacttagatatgttttattatgcagctatctgtggtattgctatcccggactagcagttttcatgttttaggtctttcatagcttgtgtgccaaggtcctttttgtaatcagatgcatctcctaatttgcaatgccatttgacctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAAGACAAGCGTTACAAGAACCGCGAACTGCAGACCATGCGCCTCCTTGACC
                                                                                                 || ||| ||   ||||   |  |     ||    | || | |     ||     | |  ||||    |     |||||||||| |||||||| || || || || || || || ||||| || ||||||||||| ||||||||||| || || ||||  ||||||||||| ||||
-----------------------------------------------------------------------------------------------gtattgctagt---ccaaa--cagtgcaacaaaagcaggcttttatcgtttcttctttctctttgg---gaatgcagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGCTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

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|67039601|gb|CO465856.1|CO465856
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
EST: gi|22819758|gb|BU499848.1|BU499848
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
EST: gi|211304795|gb|FL143344.1|FL143344
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAA
EST: gi|87156577|gb|DY401366.1|DY401366
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
EST: gi|211304794|gb|FL143343.1|FL143343
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTT
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTT
EST: gi|24773942|gb|CA409196.1|CA409196
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
EST: gi|26559736|gb|CA831971.1|CA831971
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
EST: gi|32865540|gb|CF005222.1|CF005222
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTC
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTC
EST: gi|32931957|gb|CF036769.1|CF036769
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA
EST: gi|32933926|gb|CF038738.1|CF038738
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCACAAAGAAGGTTCTTCAA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAGgttagttgca ... ctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttgtaatcagatgcatctcctaatttgcaatgccatttgacctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAAGACAAGCGTTACAAGAACCGCGAACTGCAGACCATGCGCCTCCTTGACC
                                            cctgttc  CT-rich tract
                        taattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttgcaacaactcctgacttagatatgttttattatgcagctatctgtggtattgctatcccggactagcagttttcatgttttaggtctttcatagcttgtgtgccaaggtcctttttgtaatcagatgcatctcctaatttgcaatgccatttgacctgttcatagGCCAAGTGTTTGGAAACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAAGACAAGCGTTACAAGAACCGCGAACTGCAGACCATGCGCCTCCTTGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG