RetrogeneDB ID: retro_cfam_1828

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:56813034..56813640(-)
• Located in intron of: ENSCAFG00000020161

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKB
• Ensembl ID: ENSCAFG00000018277
• Aliases: None
• Description: Creatine kinase B-type [Source:UniProtKB/Swiss-Prot;Acc:P05124]

Sequence

>retro_cfam_1828
GAGGCGGAGCAGCAGCAGCTCATTGACAACCACTTCCTCTTTGATAAGCCCATGTCACCCCTGCTCCTGGCCTCGGGCAT
GGCCTGCGACTGGCCAGATGCCTGTGGCATCTGGCACAATGACAATAAGACCTTCCTGGTGTGGATCAACGAGGAAGACC
ACCTGCAGGTCATCTCCATGCAGAAAGGGGGCAACATGAAGGAGGTGTTCGCTCGGTTCTGCAACGACCTCACCCAGATT
GAAACACTTTTCAAGTCGAAGAATTATGAATTCATGTGGAACCCTCACCTGGGCTACATCCTCACCTCCCCATCCAACTT
GGGCACAGGCCTGCGGGCAGGTGTGCACATCAAGCTGCCCCTCCTGGGCAAGCATGAGAAGTTCCTGGAGGTGCTCAAGC
GGCTGCGGCTTCAGAAATGAGGCACAGGTGGTGTGGACACAGCTGCTGTGGGTGGTGTCTTTGATGTCTCCAACGCAGAC
CGCCTGGGCTTCTCAGAGGTGGAGCTGGTACAGATGGTGGTGGATGGTGTGAAGCTGCTCAGTGAGATGGAGCAGCATCT
GCCACCACCACCAGCCCCACTGCTTCCTAACTTATTGCCCGGGCAG

Alignment

ORF - retro_cfam_1828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.12 %
• Parental protein coverage: 52.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EAEQQQLIDDHFLFDKPVSPLLLASGMARDWPDARGIWHNDNKTFLVWINEEDHLRVISMQKGGNMKEVF
          EAEQQQLID.HFLFDKP.SPLLLASGMA.DWPDA.GIWHNDNKTFLVWINEEDHL.VISMQKGGNMKEVF
Retrocopy EAEQQQLIDNHFLFDKPMSPLLLASGMACDWPDACGIWHNDNKTFLVWINEEDHLQVISMQKGGNMKEVF

Parental  TRFCNGLTQIETLFKSKNYEFMWNPHLGYILTCPSNLGTGLRAGVHIKLPHLGKHEKFPEVLKRLRLQKR
          .RFCN.LTQIETLFKSKNYEFMWNPHLGYILT.PSNLGTGLRAGVHIKLP.LGKHEKF.EVLKRLRLQK.
Retrocopy ARFCNDLTQIETLFKSKNYEFMWNPHLGYILTSPSNLGTGLRAGVHIKLPLLGKHEKFLEVLKRLRLQK*

Parental  GTGGVDTAAVGGVFDVSNADRLGFSEVELVQMVVDGVKLLIEMEQRLEQGQA--IDDLVPAQ
          GTGGVDTAAVGGVFDVSNADRLGFSEVELVQMVVDGVKLL.EMEQ.L....A.....L.P.Q
Retrocopy GTGGVDTAAVGGVFDVSNADRLGFSEVELVQMVVDGVKLLSEMEQHLPPPPAPLLPNLLPGQ

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	509.03 RPM
SRP017611_brain	0.00 RPM	507.87 RPM
SRP017611_kidney	0.00 RPM	66.37 RPM
SRP017611_liver	0.00 RPM	8.70 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1828 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1828 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1828 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018277	5 retrocopies	retro_cfam_1828 , retro_cfam_2061, retro_cfam_2159, retro_cfam_274, retro_cfam_664,
Ciona intestinalis	ENSCING00000007141	1 retrocopy	retro_cint_27,
Echinops telfairi	ENSETEG00000008667	1 retrocopy	retro_etel_1667,
Macropus eugenii	ENSMEUG00000002979	3 retrocopies	retro_meug_1069, retro_meug_1569, retro_meug_2156,
Mus musculus	ENSMUSG00000001270	4 retrocopies	retro_mmus_1460, retro_mmus_1578, retro_mmus_1647, retro_mmus_2390,
Oryctolagus cuniculus	ENSOCUG00000008818	1 retrocopy	retro_ocun_1562,
Sarcophilus harrisii	ENSSHAG00000016459	2 retrocopies	retro_shar_432, retro_shar_645,