RetrogeneDB ID: retro_cfam_1313

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:28970197..28970593(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX1
• Ensembl ID: ENSCAFG00000004567
• Aliases: None
• Description: Canis lupus familiaris peroxiredoxin 1 (PRDX1), mRNA. [Source:RefSeq mRNA;Acc:NM_001252165]

Sequence

>retro_cfam_1313
CAACTCAACTGTCAAGTGATTGGTGCTTCTGTGGATTCTCATTTCTGTCACCTGGCTTGGATCAACACACCCAAGAAACA
AGGAGGACTGGGACCCATGAACATTCCCTTGGTATCAGACCCCAAGCGTACCATTGCTCAGGACTATGGAGTCTTAAAGG
TTGATGAAGGCATCTCGTTCAGGGGCCTCTTTATTATTGATGATAAAGGTATCCTTCGGCAGATCACTGTAAATGACCTT
CCTGTTGGTCGCTCTGTGGATGAGACTCTGCGACTAGTTCAGGCCTTCCAGTTTACTGACAAGCATGGGGAAGTGTGCCC
AGCTGGCTGGAAGCCTGGCAGTGATACCATCAAGCCTGATGTCCAGAAGAGCAAAGAATACTTCTCTAAGCAGAAG

Alignment

ORF - retro_cfam_1313 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.48 %
• Parental protein coverage: 66.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKG
          .LNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLK.DEGISFRGLFIIDDKG
Retrocopy QLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKVDEGISFRGLFIIDDKG

Parental  ILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVQKSKEYFSKQK
          ILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVQKSKEYFSKQK
Retrocopy ILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVQKSKEYFSKQK

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	90.97 RPM
SRP017611_brain	0.16 RPM	62.40 RPM
SRP017611_kidney	0.33 RPM	572.01 RPM
SRP017611_liver	0.07 RPM	149.81 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1313 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1313 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1313 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 32 parental genes, and 90 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013632	2 retrocopies	retro_amel_1116, retro_amel_539,
Bos taurus	ENSBTAG00000003642	2 retrocopies	retro_btau_1299, retro_btau_1446,
Canis familiaris	ENSCAFG00000004567	5 retrocopies	retro_cfam_1313 , retro_cfam_270, retro_cfam_577, retro_cfam_834, retro_cfam_988,
Canis familiaris	ENSCAFG00000012109	3 retrocopies	retro_cfam_1322, retro_cfam_219, retro_cfam_9,
Canis familiaris	ENSCAFG00000017163	3 retrocopies	retro_cfam_1603, retro_cfam_1624, retro_cfam_1739,
Choloepus hoffmanni	ENSCHOG00000003358	5 retrocopies	retro_chof_1140, retro_chof_134, retro_chof_1714, retro_chof_2035, retro_chof_2450,
Ciona intestinalis	ENSCING00000003002	1 retrocopy	retro_cint_8,
Callithrix jacchus	ENSCJAG00000004807	2 retrocopies	retro_cjac_1201, retro_cjac_2884,
Cavia porcellus	ENSCPOG00000014137	3 retrocopies	retro_cpor_1079, retro_cpor_290, retro_cpor_398,
Dasypus novemcinctus	ENSDNOG00000018488	1 retrocopy	retro_dnov_2071,
Dipodomys ordii	ENSDORG00000008975	1 retrocopy	retro_dord_727,
Equus caballus	ENSECAG00000008678	1 retrocopy	retro_ecab_81,
Echinops telfairi	ENSETEG00000007922	11 retrocopies	retro_etel_112, retro_etel_1157, retro_etel_1245, retro_etel_1442, retro_etel_1838, retro_etel_2121, retro_etel_2122, retro_etel_308, retro_etel_367, retro_etel_460, retro_etel_556,
Felis catus	ENSFCAG00000028484	1 retrocopy	retro_fcat_1714,
Homo sapiens	ENSG00000117450	1 retrocopy	retro_hsap_4230,
Macropus eugenii	ENSMEUG00000006820	4 retrocopies	retro_meug_1694, retro_meug_1711, retro_meug_2059, retro_meug_662,