RetrogeneDB ID: retro_cfam_843

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:19343330..19344259(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: WASH4P
• Ensembl ID: ENSCAFG00000015743
• Aliases: None
• Description: WAS protein family homolog 4 pseudogene [Source:HGNC Symbol;Acc:14126]

Sequence

>retro_cfam_843
GTGACTCCGGTGAGGACCCAGCACTCGTTGGCAGGGCAGACCTATGCAGTGCCCCTCATCCAGCCGGACCTGTGGCGGGG
GGAGGCCATCCAGCAGATGGCAGATGCCCTGCAGTACCTACAGAAGGCTCTGGAGACATCTTTAGCAGGATCTCCCAACG
AGTAGAGCTCAGCCGGAAGCAGCTGCAGGCCATTGGGGAGAGGGTCTCCAGGCCAAGATCGAGAAGATTAAGGGCAGCAA
GAAGGCGATCAAGGTGTTCTCCAGTGCCAAGTACCCAGCTCCAGAGCGCTTACAGGAGTAGGATTCCATCTTCACGGATG
CCCAGGACCCAGGACTGCAGAGACGCCCTTGCCATAGCATCCAGAGCAAGCACCGCCCCCTGGATGAGTGGGCCCTGCAG
AAGCTGAAATACTTCGCTGTGTGTGTGAACACCAAGCCAGAGCCTGAGGATGAGGCCGAGGAGGGGCTTGGGGGTCTTCC
CAGCGACATCAGATCCGTCAGCTCGTTGCTGCTATTCAACACCACTGAGAACCTGAACAAAAAGTATGTCTTCTTGGACC
CCCTGGCTGGTGCTGTAACAAAGACCCATGTGATGCTGGGGGCAGAGACAGAGGAGAAGTTGTTCGATGCCCCTTTGTCC
ATCAGCAAGAGGGAGCAGCTGGAGCAACAGGTTCCAGAAAACTACTTCTGTGTGCCTGACCTGGGCCAAGTGCCTGAGAT
TGATGTGCCATCCTACCTGCCCGACCTGCCGGGCATTGCCGATGACCTCATGTACAGTGCTGACCTGGGCCCTGGCATCG
CCCCTCCGCCCCTGGCACCATTCCAGAGCTGCCCACCTTCCACACAGAGGTGGCTGAGACTTTCAAGCCAGACCTGGAAG
ATGCGGAACTATACTAACAGCACCTACGCCGCCGCCGTCACCACCCCCA

Alignment

ORF - retro_cfam_843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.79 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MTPMRTQHSLAGQTYAVPLIQPDLRREEAIQQMADALQYLQKV-SGDIFSRISQRVELSRKQLQAIGERV
          .TP.RTQHSLAGQTYAVPLIQPDL.R.EAIQQMADALQYLQK..SGDIFSRISQRVELSRKQLQAIGERV
Retrocopy VTPVRTQHSLAGQTYAVPLIQPDLWRGEAIQQMADALQYLQKA<SGDIFSRISQRVELSRKQLQAIGERV

Parental  SLAQAKIEKIKGSKK-AIKVFSSAKYPAPERLQEYDSIFTGAQDPGLQRRPRYRIQSKHRPLDEWALQEK
          S...............AIKVFSSAKYPAPERLQE.DSIFT.AQDPGLQRRP...IQSKHRPLDEWALQ.K
Retrocopy SRPRSR--RLRAARR<AIKVFSSAKYPAPERLQE*DSIFTDAQDPGLQRRPCHSIQSKHRPLDEWALQ-K

Parental  LKYFPVCVNTKPEPEDEAEEGLGGLPSNISSVSSLLLFNTTENLYKKYVFLDPLAGAVTKTHVMLGAETE
          LKYF.VCVNTKPEPEDEAEEGLGGLPS.I.SVSSLLLFNTTENL.KKYVFLDPLAGAVTKTHVMLGAETE
Retrocopy LKYFAVCVNTKPEPEDEAEEGLGGLPSDIRSVSSLLLFNTTENLNKKYVFLDPLAGAVTKTHVMLGAETE

Parental  EKLFDAPLSISKREQLEQQVPENYFYVPDLGQVPEIDVPSYLPDLPGIADDLMYSADLGPGIA-PSAPGT
          EKLFDAPLSISKREQLEQQVPENYF.VPDLGQVPEIDVPSYLPDLPGIADDLMYSADLGPGIA.PSAPGT
Retrocopy EKLFDAPLSISKREQLEQQVPENYFCVPDLGQVPEIDVPSYLPDLPGIADDLMYSADLGPGIA<PSAPGT

Parental  IPELPTFHTEVAETFKPDLEDGVL-TAPPPPPPPPPPP
          IPELPTFHTEVAETFKPDLED..L.....P.PPP.PPP
Retrocopy IPELPTFHTEVAETFKPDLEDAEL<ILTAPTPPPSPPP

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	0.04 RPM	16.30 RPM
SRP017611_brain	0.00 RPM	20.96 RPM
SRP017611_kidney	0.07 RPM	39.56 RPM
SRP017611_liver	0.00 RPM	16.03 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_843 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_843 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015743	1 retrocopy	retro_cfam_843 ,
Macropus eugenii	ENSMEUG00000003621	1 retrocopy	retro_meug_1409,