RetrogeneDB ID: retro_cfam_643

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:54780119..54780650(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC10
• Ensembl ID: ENSCAFG00000031203
• Aliases: None
• Description: zinc finger, CCHC domain containing 10 [Source:HGNC Symbol;Acc:25954]

Sequence

>retro_cfam_643
ATGGCAACTCCCATGCATCGGCTCATAGCTCAGAGACAAGCTGAAGCAAATGAACAGCATGTAAGATGTCAGAAATGCTT
GGAATTTAGACACTGGACTTATGAATGCACCGGAAAAAGAAAATACCTGCATAGGCCTTCAAGGACAGCAGAACTAAAGA
AAGCTTTAAAAGAAAAAGGAAACAGATTATTATTATTACTGCAACAAAGCATCAGAGAAACTAATGTAGAAAGGAAGACC
AAGAGAAAAAGGTCTAAGAGTGTAACCAGTTCCAGCAGCAGTAGCAGCGACAGTTCAGCCAGTGGTTCTTCATCAGAAAA
GTGAAGAAACCTCTCCATCCTCCTCCTCAGAGGACAGCGACACCACCCCACTGATGAAAGCTCCTCCAGTTCCTCATCTT
CATCCTCCTCCACAACCTCTTCCTCCTCCTCTGATTCAGACTCAGATTCCAGCTCTTCCAGGAGCAGCAGCACCAGCACC
AGCACAGAGAGCAGCTCTGAGGATGAACCACCAAAGAAGAAGAAAAAGAAA

Alignment

ORF - retro_cfam_643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATPMHRLIARRQAEANKQHVRCQKCLEFGHWTYECTGKRKYLHRPSRTAELKKALKEKENRLLLL-QQS
          MATPMHRLIA.RQAEAN.QHVRCQKCLEF.HWTYECTGKRKYLHRPSRTAELKKALKEK.NRLLLL.QQS
Retrocopy MATPMHRLIAQRQAEANEQHVRCQKCLEFRHWTYECTGKRKYLHRPSRTAELKKALKEKGNRLLLLLQQS

Parental  IGETNVERKTKKKRSKSVTSSSSS---SSDSSASDS-SSESEETSTSSSSEDSD-TDESSSSSSSSSSST
          I.ETNVERKTK.KRSKSVTSSSSS...SS.S..S...S.E....S.S..S.....TDE............
Retrocopy IRETNVERKTKRKRSKSVTSSSSSSSDSSASGSSSE>SEETSPSSSSEDSDTTP<TDEXXXXXXXXXXXX

Parental  SSSSSSDSDSDSSSS--SSSSTSTESSSEDEPPKKKKKK
          .......SDSDSSSS..SS.STSTESSSEDEPPKKKKKK
Retrocopy XXXXXXXSDSDSSSSRSSSTSTSTESSSEDEPPKKKKKK

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	0.00 RPM	4.87 RPM
SRP017611_brain	0.00 RPM	3.73 RPM
SRP017611_kidney	0.00 RPM	10.70 RPM
SRP017611_liver	0.00 RPM	1.89 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_643 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_643 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031203	1 retrocopy	retro_cfam_643 ,
Choloepus hoffmanni	ENSCHOG00000001420	9 retrocopies	retro_chof_1243, retro_chof_1263, retro_chof_1773, retro_chof_2048, retro_chof_2132, retro_chof_2183, retro_chof_501, retro_chof_790, retro_chof_923,
Dasypus novemcinctus	ENSDNOG00000017302	1 retrocopy	retro_dnov_257,
Myotis lucifugus	ENSMLUG00000011366	4 retrocopies	retro_mluc_172, retro_mluc_2240, retro_mluc_2241, retro_mluc_2574,
Monodelphis domestica	ENSMODG00000013827	1 retrocopy	retro_mdom_1405,
Mus musculus	ENSMUSG00000018239	1 retrocopy	retro_mmus_269,
Otolemur garnettii	ENSOGAG00000032171	1 retrocopy	retro_ogar_3011,
Rattus norvegicus	ENSRNOG00000006943	3 retrocopies	retro_rnor_2037, retro_rnor_2528, retro_rnor_801,