RetrogeneDB ID: retro_cfam_1427

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:39868064..39868902(-)
• Located in intron of: ENSCAFG00000018143

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE4A
• Ensembl ID: ENSCAFG00000012419
• Aliases: None
• Description: non-SMC element 4 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:25935]

Sequence

>retro_cfam_1427
GAAAACCGGGAGGATATACTGAATGCCAGAGACAAATTAACAGAGGTCCTTGAAGAGGCCAACACTCTGTTTAATGGAGT
GTCCCGAGCAAGAGAAGCAGTCCTAGATGCCCAGTTTCTCGTTTTGGCTTCAGATTTGGGCAAAGAGAAAGCAAAGCAAC
TGCGTTCTGATCTGAACTCATTTGATATGTTAAGATATGTTGAAACTCTACAGACACATATGGGTGTAAATCCACTAGAA
GCTGAAGAACTCATCCGTGATGAAGATAGTTCTGATTTTGAATTCATAGTCTATGACTCCTGGAAAATATCAGGCAAAAG
AGCAGAAAACACCTTTAGTAAAACCCATACATTCCACTTCTGTTGGGTTCAATACAAGGAGAGTTCCCTGTGCCAAAGCC
ACGAAGTGAACGTCCAAGAAAAGGTCCCACGACAGAATAGAAGACAATGCCTGACCAGTTAAGTGAAATGGAAGAATCAC
ATCAAGAAGCGACAGAGAAAGAAGTGGAAAGAATTTTGGGATTGTTGCAGACATATTTCCGAGAAGATCCCGATACTCCT
ATGTTGTTCTTTAATTTTGTGGTTGATCCACATTCTTTCCCCCGAATAGCAGAAAACATCTTTCATGTTTCCTTCATTAT
AAGGGATGGTTTTGCAAGAATAAAGCTTGACCAAGACCGACTACCAATAATAGAACCTGTTAATATTAATGAAGAAAGTG
AGGGAATTGACCAAAACACCCAAATTAGGAATCAAGGAATTATAGCTCTGAGCTACCGTGACTGGGAGGAGATGTGAAGA
CCTTCGAGATATCAGAGCCTGTGATTGCTTCAGGCCAA

Alignment

ORF - retro_cfam_1427 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ENREDILNASDKLTEVLEEANTLFNGVSRAREAVLDAQFLVLASDLGKEKAKQLRSDLNSFDMLRYVETL
          ENREDILNA.DKLTEVLEEANTLFNGVSRAREAVLDAQFLVLASDLGKEKAKQLRSDLNSFDMLRYVETL
Retrocopy ENREDILNARDKLTEVLEEANTLFNGVSRAREAVLDAQFLVLASDLGKEKAKQLRSDLNSFDMLRYVETL

Parental  LTHMGVNPLEAEELIRDEDSSDFEFIVYDSWKISGKTAENTFNKTHTFHF-LLGSIQGEFPVPKPRSERP
          .THMGVNPLEAEELIRDEDSSDFEFIVYDSWKISGK.AENTF.KTHTFHF.LLGSIQGEFPVPKPRSERP
Retrocopy QTHMGVNPLEAEELIRDEDSSDFEFIVYDSWKISGKRAENTFSKTHTFHF<LLGSIQGEFPVPKPRSERP

Parental  RKGPTTEEKKTMPDQLSEMEESHQEATEKEVERILGLLQTYFREDPDTPMSFFDFVVDPHSFPRTVENIF
          RKGPTT.E.KTMPDQLSEMEESHQEATEKEVERILGLLQTYFREDPDTPM.FF.FVVDPHSFPR..ENIF
Retrocopy RKGPTT-E*KTMPDQLSEMEESHQEATEKEVERILGLLQTYFREDPDTPMLFFNFVVDPHSFPRIAENIF

Parental  HVSFIIRDGFARIKLDQDRLPIIETEPVNINEESEGIDQNTQIRNQGIIALSYRDWEEI-VKTFEISEPV
          HVSFIIRDGFARIKLDQDRLPII..EPVNINEESEGIDQNTQIRNQGIIALSYRDWEE..VKTFEISEPV
Retrocopy HVSFIIRDGFARIKLDQDRLPII--EPVNINEESEGIDQNTQIRNQGIIALSYRDWEEM<VKTFEISEPV

Parental  IASGQ
          IASGQ
Retrocopy IASGQ

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	0.08 RPM	9.53 RPM
SRP017611_brain	0.08 RPM	5.80 RPM
SRP017611_kidney	0.26 RPM	7.92 RPM
SRP017611_liver	0.15 RPM	5.15 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1427 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1427 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1427 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010897	1 retrocopy	retro_amel_419,
Bos taurus	ENSBTAG00000019166	1 retrocopy	retro_btau_1387,
Canis familiaris	ENSCAFG00000012419	2 retrocopies	retro_cfam_1427 , retro_cfam_379,
Choloepus hoffmanni	ENSCHOG00000003695	1 retrocopy	retro_chof_577,
Dipodomys ordii	ENSDORG00000003880	1 retrocopy	retro_dord_677,
Equus caballus	ENSECAG00000016651	2 retrocopies	retro_ecab_109, retro_ecab_465,
Erinaceus europaeus	ENSEEUG00000014906	1 retrocopy	retro_eeur_124,
Felis catus	ENSFCAG00000003647	1 retrocopy	retro_fcat_994,
Homo sapiens	ENSG00000107672	1 retrocopy	retro_hsap_43,
Loxodonta africana	ENSLAFG00000004214	1 retrocopy	retro_lafr_1051,
Macaca mulatta	ENSMMUG00000012044	1 retrocopy	retro_mmul_716,
Mustela putorius furo	ENSMPUG00000002960	1 retrocopy	retro_mputfur_396,
Nomascus leucogenys	ENSNLEG00000016919	1 retrocopy	retro_nleu_2073,
Otolemur garnettii	ENSOGAG00000010026	1 retrocopy	retro_ogar_280,
Pongo abelii	ENSPPYG00000002712	1 retrocopy	retro_pabe_878,
Pteropus vampyrus	ENSPVAG00000017186	2 retrocopies	retro_pvam_1163, retro_pvam_795,
Rattus norvegicus	ENSRNOG00000020452	1 retrocopy	retro_rnor_2515,
Ictidomys tridecemlineatus	ENSSTOG00000011112	1 retrocopy	retro_itri_36,
Vicugna pacos	ENSVPAG00000006534	1 retrocopy	retro_vpac_260,