RetrogeneDB ID: retro_cfam_1931

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:2838849..2839990(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000011124
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: THAP5
• Ensembl ID: ENSCAFG00000003290
• Aliases: None
• Description: THAP domain containing 5 [Source:HGNC Symbol;Acc:23188]

Sequence

>retro_cfam_1931
AGGAACCATCGGGGACGAAAGCTGAGTTGTTACCCGTTTCCTCTACATGGCAAAGAAAGACTTGAAAAATGGTTAAAGAA
TATGAAACGAGATTCATGGGTACCCAGGAAATACCAGTTCCTGTGTAGTGACCATTTTACTCCTGACTCTCTTGACATCA
GATGGGGTATTCGATATTTGAAACAAACTGCAATTCCAACAATATTTTCTTTGCCTGAAGACGATCAGGACAAAGACCCT
TCCAAAAAAAAAAATCTCAGAAGAAAAAAATTAGATGATGAGAAAGAAGTGTGCCTAAAAGCCAAGTCACAAGAATCATT
TGCTTCAAATGAGTTAAAGAAAAATACGGTTAATACAAATATCCTCCCTGAACACACAGAATTACGTAATTCATCTACTT
TGGTGAAGCCACCAGCTGCCAAACCAGAATGTATACAAAATAACATATTAAATCTTAATCTGCTTAAACAAGATATTGGA
ATACCAGTATCTACCTTGGAAACTTCAGTTACCCAAGACATAGATATAGGTGGTTTTCACACATTTTTTGAGAATCTAAA
TTCTACAACTATTACCTTGACAACTTCAAACTCTGAAGATGTTCAGCCGTTTTTGGAAACCCAAGAAGTGTTTGAAATAA
CTGCGAATCATCTTGCTAACCCAAACTTTACAAATAATTCCATGGAAATTAAGTCTGCACAGGAAAGTCCATTTTTACTC
AGCACAATTACTCAAACAGTCGAAGAGTTAAATACAAATAAAGAATCTGTTATTGCCATTTTTGTACCCACAGAAAATTC
CAAACCAATTAATTCTTTTGTATCTGCTGAAAAAGAAACTGTGGAAATGGAAGATCTAGACATTGAAGACTCCTTATATA
AGGATGTAGACTATGAGACAGAAGTTTTACAAATTGAACATTCTTACTGCAGACAAGATATAAATAAGGAACATCTTTGG
CAGAAAGTTTCTAAACTACATTCAAAGATAACTCTTCTCCAGCTACAAGAACAACAAACTCTTGGAAGATTGAAGTCTTT
GGAAGCTCTTATAAGTCAGCTAAAACAAGAAAACTGGCTATCTGAAGAAAATGTCAAAGATTATAGAAAATCATTTCACA
ACATATGAAGTTACCATGATA

Alignment

ORF - retro_cfam_1931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.7 %
• Parental protein coverage: 95.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RNSKDRKLSFYPFPLHDKERLEKWLKNMKRDSWVPSKYQFLCSDHFTPDSLDIRWGIRYLKQTAIPTIFS
          RN...RKLS.YPFPLH.KERLEKWLKNMKRDSWVP.KYQFLCSDHFTPDSLDIRWGIRYLKQTAIPTIFS
Retrocopy RNHRGRKLSCYPFPLHGKERLEKWLKNMKRDSWVPRKYQFLCSDHFTPDSLDIRWGIRYLKQTAIPTIFS

Parental  LPEDDQEKDPSKKKS-QKKKLDDEKEVCLKAKSQESFASNELKKNTVNTNILLEHTELCNSSTLVKPPAP
          LPEDDQ.KDPS.......KKLDDEKEVCLKAKSQESFASNELKKNTVNTNIL.EHTEL.NSSTLVKPPA.
Retrocopy LPEDDQDKDPSXXXXLRRKKLDDEKEVCLKAKSQESFASNELKKNTVNTNILPEHTELRNSSTLVKPPAA

Parental  KPECIQNNVLTLNLLKQDIGIPVSTLETSVTQDIDIGGFHTSFENLNSTTITLTTSNSEDVQPSLETQEV
          KPECIQNN.L.LNLLKQDIGIPVSTLETSVTQDIDIGGFHT.FENLNSTTITLTTSNSEDVQP.LETQEV
Retrocopy KPECIQNNILNLNLLKQDIGIPVSTLETSVTQDIDIGGFHTFFENLNSTTITLTTSNSEDVQPFLETQEV

Parental  FEITANHLANPNFTNNSMEIKSAQESPFLLSTITQTVEELNTNKESVIAIFVPTENSKPINSFVSAEKET
          FEITANHLANPNFTNNSMEIKSAQESPFLLSTITQTVEELNTNKESVIAIFVPTENSKPINSFVSAEKET
Retrocopy FEITANHLANPNFTNNSMEIKSAQESPFLLSTITQTVEELNTNKESVIAIFVPTENSKPINSFVSAEKET

Parental  VEMEDLDIEDSLYKDVDYETEVLQIEHSYCRQDINKEHLWQKVSKLHSKITLLELQEQQTLGRLKSLEAL
          VEMEDLDIEDSLYKDVDYETEVLQIEHSYCRQDINKEHLWQKVSKLHSKITLL.LQEQQTLGRLKSLEAL
Retrocopy VEMEDLDIEDSLYKDVDYETEVLQIEHSYCRQDINKEHLWQKVSKLHSKITLLQLQEQQTLGRLKSLEAL

Parental  IRQLKQENWLSEENV-KIIENHFTTYEVTMI
          I.QLKQENWLSEENV.KIIENHFTTYEVTMI
Retrocopy ISQLKQENWLSEENV>KIIENHFTTYEVTMI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.42 RPM	23.35 RPM
SRP017611_brain	0.64 RPM	20.48 RPM
SRP017611_kidney	1.06 RPM	35.92 RPM
SRP017611_liver	0.07 RPM	8.99 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1931 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1931 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1931 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000456	1 retrocopy	retro_cfam_2005,
Canis familiaris	ENSCAFG00000003290	1 retrocopy	retro_cfam_1931 ,
Homo sapiens	ENSG00000177683	1 retrocopy	retro_hsap_3924,
Myotis lucifugus	ENSMLUG00000015130	1 retrocopy	retro_mluc_1285,
Nomascus leucogenys	ENSNLEG00000008290	1 retrocopy	retro_nleu_2994,