RetrogeneDB ID: retro_cfam_1297

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:1193009..1193618(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000030350
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PGAM4
• Ensembl ID: ENSCAFG00000009062
• Aliases: None
• Description: phosphoglycerate mutase family member 4 [Source:HGNC Symbol;Acc:21731]

Sequence

>retro_cfam_1297
GCTGGCTAGGAGTTTGACATTTGCTTTACCTCAGTGCAGAAGAGAGCAATTCAGACAGTGCTGAATTCCATTGGCCAAAT
GTGGCTGCCAGTAGTGAGGACCTGGCACTCCAGTGAGTGACACTATGGGGTTCTGACTGGCCTCAATAAAGCAGAAACTA
CTGCCAAGCATGGCGAGACCCAGAAAAGAACTGGAGATGCTCTTATGATGCCCTACCACCTCTGATGGAGCCTGACCATC
CCTTCTACAGCAACATTAGTAAGAATCACAGGTGTGCAGAGTTCATTGAATATCCCCTACCCTCCTGTGAGAGTCTAAAG
TACACAGTTGCCAGAACTATGCCCTTTTAGAAAGAAGAAATACCCCCAGATCAAAGAGGGGAAATGGGTACAGATTGTAG
CCCATGGCAACAACCTTCTGGACATTGTCAAGCATCTGGAGGGTCTTTCCAAAGAAGCTATCATTGAGCTGAACCTGCCA
ACTAGTATTCCCATGGTCTATGAATTAGACAAGAACTTTAAGCCCATCAAGACCAGACAGTTCCTGGGGGATGAAGAGAA
CATGGGTAAAGCCATGGAAGCTGTGGCTGCCCAGAGGAAAGCCAAAAAG

Alignment

ORF - retro_cfam_1297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 81.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGYEFDICFTSVQKRAIRTLWTVLDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQV-KIWR
          AG.EFDICFTSVQKRAI....TVL..I.QMWLPVVRTW...E.HYG.LTGLNKAET.AKHGE.Q..K.WR
Retrocopy AG*EFDICFTSVQKRAIQ---TVLNSIGQMWLPVVRTWHSSE*HYGVLTGLNKAETTAKHGETQK<KNWR

Parental  RSYDVPPPPMEPDHPFYSNISKDRRYADLTEDQLPSCESLKDTIARAL-PFWNEEIVPQIKEGKRVLIAA
          .SYD..PP.MEPDHPFYSNISK..R.A...E..LPSCESLK.T.AR...PF......PQIKEGK.V.I.A
Retrocopy CSYDALPPLMEPDHPFYSNISKNHRCAEFIEYPLPSCESLKYTVARTM>PFRKKKY-PQIKEGKWVQIVA

Parental  HGNSLRGIVKHLEGLSEEAIMELNLPTGIPMVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQGKAKK
          HGN.L..IVKHLEGLS.EAI.ELNLPT.IPMVYELDKN.KPIK..QFLGDEE...KAMEAVAAQ.KAKK
Retrocopy HGNNLLDIVKHLEGLSKEAIIELNLPTSIPMVYELDKNFKPIKTRQFLGDEENMGKAMEAVAAQRKAKK

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	140.95 RPM
SRP017611_brain	0.00 RPM	247.47 RPM
SRP017611_kidney	0.00 RPM	261.57 RPM
SRP017611_liver	0.00 RPM	54.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1297 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1297 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1297 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012697	2 retrocopies	retro_btau_1611, retro_btau_472,
Canis familiaris	ENSCAFG00000009062	1 retrocopy	retro_cfam_1297 ,
Callithrix jacchus	ENSCJAG00000016575	1 retrocopy	retro_cjac_370,
Erinaceus europaeus	ENSEEUG00000005630	1 retrocopy	retro_eeur_680,
Echinops telfairi	ENSETEG00000002467	1 retrocopy	retro_etel_1595,
Homo sapiens	ENSG00000171314	12 retrocopies	retro_hsap_1048, retro_hsap_1052, retro_hsap_1142, retro_hsap_2235, retro_hsap_2604, retro_hsap_3083, retro_hsap_3488, retro_hsap_4249, retro_hsap_4686, retro_hsap_4821, retro_hsap_885, retro_hsap_913,
Gorilla gorilla	ENSGGOG00000028602	13 retrocopies	retro_ggor_1220, retro_ggor_1500, retro_ggor_1667, retro_ggor_1824, retro_ggor_2061, retro_ggor_2118, retro_ggor_2353, retro_ggor_2849, retro_ggor_3005, retro_ggor_3034, retro_ggor_716, retro_ggor_738, retro_ggor_827,
Loxodonta africana	ENSLAFG00000015979	1 retrocopy	retro_lafr_886,
Microcebus murinus	ENSMICG00000007657	1 retrocopy	retro_mmur_135,
Myotis lucifugus	ENSMLUG00000009117	6 retrocopies	retro_mluc_1280, retro_mluc_1595, retro_mluc_1741, retro_mluc_2246, retro_mluc_632, retro_mluc_745,
Macaca mulatta	ENSMMUG00000020027	1 retrocopy	retro_mmul_119,
Monodelphis domestica	ENSMODG00000004242	4 retrocopies	retro_mdom_1342, retro_mdom_1893, retro_mdom_610, retro_mdom_668,
Mus musculus	ENSMUSG00000011752	6 retrocopies	retro_mmus_1741, retro_mmus_2221, retro_mmus_3012, retro_mmus_411, retro_mmus_729, retro_mmus_769,
Nomascus leucogenys	ENSNLEG00000013804	10 retrocopies	retro_nleu_1367, retro_nleu_1535, retro_nleu_1658, retro_nleu_2012, retro_nleu_2139, retro_nleu_2196, retro_nleu_2205, retro_nleu_2488, retro_nleu_2667, retro_nleu_280,
Oryctolagus cuniculus	ENSOCUG00000005679	5 retrocopies	retro_ocun_1016, retro_ocun_1081, retro_ocun_350, retro_ocun_706, retro_ocun_976,
Rattus norvegicus	ENSRNOG00000050585	7 retrocopies	retro_rnor_1669, retro_rnor_2241, retro_rnor_2275, retro_rnor_2361, retro_rnor_2568, retro_rnor_691, retro_rnor_703,
Sarcophilus harrisii	ENSSHAG00000018230	1 retrocopy	retro_shar_323,
Tupaia belangeri	ENSTBEG00000005913	5 retrocopies	retro_tbel_1677, retro_tbel_1708, retro_tbel_2756, retro_tbel_3667, retro_tbel_563,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,