RetrogeneDB ID: retro_cfam_2136

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:13806108..13806570(-)
• Located in intron of: ENSCAFG00000012783

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHP1
• Ensembl ID: ENSCAFG00000009525
• Aliases: None
• Description: calcineurin-like EF-hand protein 1 [Source:HGNC Symbol;Acc:17433]

Sequence

>retro_cfam_2136
ATGGGGCCTTGGGCATCCACATTACTGTAGAGGGAAGAACTAGAGGAGATCAAGCAGACCAACTTTTCTCACAGTCGGAT
CACCTACCTCTACTGCCAGTTCACCAGCCTGGACAAAGGTGAGAATGGGGCCCTCAGCTAGGATTATTTCCAGCTAATTC
CAGAACTTGTCATCAGCCCACTGGGGGCTGGTTCATTAGTGCCTTCTTTCCAGAGGGAGAAGACCAGGTAAACTTCCATG
GATTCATAAAAACTTTGGCTCAATTCCACCCCACTGAATATGGTGGAAAGAGCAAAGATAAGAATGAACCAGAAACACTC
AACAGCTGAAGCAACAAACTATACTTTGCTTTTTTGGCTATATGATTTGGATAAAGATGACAGGATCTCCCACAATGAGC
TGTTCCAGGTGCTATGCATGATGGTTGGAGTGAATATCCCAGATGAGGAACCGAGCAGCATC

Alignment

ORF - retro_cfam_2136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.43 %
• Parental protein coverage: 79.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGSRASTLLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDR-IINA
          MG..ASTLL..EELEEIK..T.FSHS.IT.LY..FTSLDKGENG.LS...FQ.IPEL.I.PLG....I.A
Retrocopy MGPWASTLL*REELEEIK-QTNFSHSRITYLYCQFTSLDKGENGALS*DYFQLIPELVISPLGAG<FISA

Parental  FFPEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFR-LYDLDKDDKISRDELLQV
          FFPEGEDQVNF.GF..TLA.F.P.E...KSKD.N.PE.LNS.SNKL.FAF..LYDLDKDD.IS..EL.QV
Retrocopy FFPEGEDQVNFHGFIKTLAQFHPTEYGGKSKDKNEPETLNS*SNKLYFAFL>LYDLDKDDRISHNELFQV

Parental  LRMMVGVNISDEQLGSI
          L.MMVGVNI.DE...SI
Retrocopy LCMMVGVNIPDEEPSSI

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	28.39 RPM
SRP017611_brain	0.00 RPM	56.92 RPM
SRP017611_kidney	0.00 RPM	26.88 RPM
SRP017611_liver	0.00 RPM	10.80 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2136 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2136 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Oryctolagus cuniculus	retro_ocun_68
Bos taurus	retro_btau_1785
Equus caballus	retro_ecab_1099

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009525	1 retrocopy	retro_cfam_2136 ,
Cavia porcellus	ENSCPOG00000010577	2 retrocopies	retro_cpor_1224, retro_cpor_726,
Homo sapiens	ENSG00000187446	2 retrocopies	retro_hsap_3334, retro_hsap_3541,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Macaca mulatta	ENSMMUG00000017092	2 retrocopies	retro_mmul_1809, retro_mmul_2088,
Mus musculus	ENSMUSG00000014077	4 retrocopies	retro_mmus_1458, retro_mmus_2094, retro_mmus_3133, retro_mmus_3469,
Nomascus leucogenys	ENSNLEG00000003465	4 retrocopies	retro_nleu_1678, retro_nleu_2269, retro_nleu_2608, retro_nleu_2609,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pan troglodytes	ENSPTRG00000006942	2 retrocopies	retro_ptro_2144, retro_ptro_2407,
Rattus norvegicus	ENSRNOG00000004742	2 retrocopies	retro_rnor_2034, retro_rnor_2223,
Ictidomys tridecemlineatus	ENSSTOG00000014503	1 retrocopy	retro_itri_227,