RetrogeneDB ID: retro_cfam_1072

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:19832507..19833049(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM92A1
• Ensembl ID: ENSCAFG00000009105
• Aliases: None
• Description: family with sequence similarity 92, member A1 [Source:HGNC Symbol;Acc:30452]

Sequence

>retro_cfam_1072
CATGAAATAAGCATGTTTGCCTCTACAGAGACCTCAAATTTAAAGCAGGGCCTGAAAAGTTTGATGAGTTTGCCACACCT
TAGGATTATCAATGAACAGAGATGGAAAGATTTGCAGCTGAAGTGGTTGAACCTTTGAAGGTTTATGGTGCCTTTGTAAA
AATGAAAGCAGATGACCTCAAAGTGACATTAATAGAAAGGAATAGAGAAGCTAAACCGTTAACTCAGGAAGAACACGTCA
GCGAAACCCTGATCACTGATGTTCAACATATCATTTCACAGGCAGAAACCAAATTGCAGAGAGTTTCTATGGATCCTCCC
TGAACAACTTGCATTCTGGAGGAAATTTTTGACAATTTTGGAAAGCAGAAAATAAAAGATATAAAGATTGTATTTTCAGA
ATGTATCATTACCAAAATGTTATTTCTTGGCAAAGCATTAAAAGTCTACACTGCTGCCTACCAGAACATACAAAAGATTG
CTGAGGAGGATTTAGAGGTTTTCCAAAATTCTCTATATCCACCAGACCATTCATCCAGTTTA

Alignment

ORF - retro_cfam_1072 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.13 %
• Parental protein coverage: 63.41 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NEINVYASTETPNLKQ-GLKNFADEFARLQDYRQAEVERLEAKVVEPLKAYGTIVKMKRDDLKATLTARN
          .EI...ASTET.NLKQ.G...F.DEFA...DY...E.ER..A.VVEPLK.YG..VKMK.DDLK.TL..RN
Retrocopy HEISMFASTETSNLKQ<GPEKF-DEFATP*DYQ*TEMERFAAEVVEPLKVYGAFVKMKADDLKVTLIERN

Parental  REAKQLNQLERTRQRNPSD-RHVISQAETELQRATMDATRTTRHLEETIDNFEKQKIKDIKTIFSEFITI
          REAK.L.Q.E........D..H.ISQAET.LQR..MD...TT..LEE..DNF.KQKIKDIK..FSE.I..
Retrocopy REAKPLTQEEHVSETLITDVQHIISQAETKLQRVSMDPP*TTCILEEIFDNFGKQKIKDIKIVFSECIIT

Parental  EMLFHGKALEVYTAAYQNIQKIDEEEDLEAFRNSLYPPDYSSRL
          .MLF.GKAL.VYTAAYQNIQKI..EEDLE.F.NSLYPPD.SS.L
Retrocopy KMLFLGKALKVYTAAYQNIQKI-AEEDLEVFQNSLYPPDHSSSL

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	16.93 RPM
SRP017611_brain	0.00 RPM	18.97 RPM
SRP017611_kidney	0.00 RPM	27.93 RPM
SRP017611_liver	0.00 RPM	2.97 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1072 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1072 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1072 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009105	1 retrocopy	retro_cfam_1072 ,
Echinops telfairi	ENSETEG00000013003	1 retrocopy	retro_etel_522,
Homo sapiens	ENSG00000188343	1 retrocopy	retro_hsap_1485,
Gorilla gorilla	ENSGGOG00000006452	1 retrocopy	retro_ggor_1137,
Loxodonta africana	ENSLAFG00000003954	1 retrocopy	retro_lafr_201,
Microcebus murinus	ENSMICG00000006797	1 retrocopy	retro_mmur_415,
Monodelphis domestica	ENSMODG00000007447	2 retrocopies	retro_mdom_1239, retro_mdom_827,
Mustela putorius furo	ENSMPUG00000009112	1 retrocopy	retro_mputfur_1183,
Nomascus leucogenys	ENSNLEG00000002773	1 retrocopy	retro_nleu_1707,
Otolemur garnettii	ENSOGAG00000002972	1 retrocopy	retro_ogar_654,
Oreochromis niloticus	ENSONIG00000002446	1 retrocopy	retro_onil_57,
Procavia capensis	ENSPCAG00000011171	1 retrocopy	retro_pcap_272,
Pongo abelii	ENSPPYG00000018744	2 retrocopies	retro_pabe_1235, retro_pabe_2497,
Tarsius syrichta	ENSTSYG00000012502	1 retrocopy	retro_tsyr_975,
Tursiops truncatus	ENSTTRG00000012378	1 retrocopy	retro_ttru_45,