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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCTAACCCTCCTCACTTCATCCATTTGTGCTACAAACCCACTGATGGGAACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagtacttgccacatatttagtgggtttatgaaaagttagaagtagacaagtagatggaaccgtttgttatttttcttatgcttggtttgccaatgaatccag

Basic information

species Zea mays
transcript GRMZM2G178958_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178958_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g55140.1 (Oryza sativa), 5'ss of exon 4
CTGCTAACCCTCCTCACTTCATCCATTTGTGCTACAAACCCACTGATGGGAACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagtacttgccacatatttagtgggtttatgaaaagttagaagtagacaagtag-atgga---accgtttgttatttttcttatgcttggtt-tgccaatgaatccag--------------
|||| || ||||| ||||||||||| ||||||||||||||  ||| |||||| | ||||||||||||||| ||||||||||||||| |||||||||||||||||||   || |    ||||||| |||   |  || |     | |  |      |||  ||  |    || | | |||| |   | ||  |||||| |  ||||  ||  |               
CTGCGAATCCTCCCCACTTCATCCACTTGTGCTACAAACCACCTGGTGGGAATGCCAAGAGAAAGCTGGCCATTGTTGGGAAGGGTCTAACTTTTGACAGgtttgtgaaacatat-gcatattttgtgaactattgcagtaacatacatcattgtgtaacataaatatgccatcttttatatggataattgttggttcttacaattgattaaccgatttttttgcag
















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|22714950|gb|BU197547.1|BU197547
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
EST: gi|148936677|gb|EC880805.2|EC880805
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACAT
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACAT
EST: gi|93012171|gb|EB637691.1|EB637691
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
EST: gi|67022782|gb|CO451531.1|CO451531
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
EST: gi|71596246|gb|DR906997.1|DR906997
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
EST: gi|67042042|gb|CO468297.1|CO468297
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
EST: gi|22472974|gb|BU037454.1|BU037454
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
EST: gi|76291680|gb|DV031248.1|DV031248
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
EST: gi|71431472|gb|DR812522.1|DR812522
EST:     AGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
genomic: AGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
EST: gi|71323796|gb|DR798569.1|DR798569
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
EST: gi|211347363|gb|FL343425.1|FL343425
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGG
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGG
EST: gi|5343060|gb|AI795470.1|AI795470
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
EST: gi|78121907|gb|DV540291.1|DV540291
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
EST: gi|71435919|gb|DR816969.1|DR816969
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
EST: gi|67023272|gb|CO452021.1|CO452021
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGAACCGG-CCANGCTGCAGCATCNAGCTGATGA
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGA-CCGGGCCAGGCTGCAGCATCGAGCTGATGA
EST: gi|5928970|gb|AW056262.1|AW056262
EST:     AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAG                         TGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA
genomic: AACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCTAACCCTCCTCACTTCATCCATTTGTGCTACAAACCCACTGATGGGAACGTCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagtacttgccacatatttagtgggtttatgaaaagttagaagtagacaagtagatggaaccgtttgttatttttcttatgcttggtttgccaatgaatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG