RetrogeneDB ID: retro_cfam_526

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:48325264..48325747(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEBP1
• Ensembl ID: ENSCAFG00000009910
• Aliases: None
• Description: phosphatidylethanolamine binding protein 1 [Source:HGNC Symbol;Acc:8630]

Sequence

>retro_cfam_526
CTCAGGTCCGTGATGTCGGTGGACCTCGGCAAGTGGTCCAGGCCTTTGAGCCTGCAAGAAGTGGAGGAGCAGCCGCAGCA
TGCGCTGCATGTCAAACACACCGGGATGGAGGTCGACGAGCTGGGCAAAGTGCTGATGCCCGCCCAGGTTAAGAACCGGC
CCACCAGTATTGCATGGGATGGTCTTGATCCAGGTAAACTCCACACCTTGGTCCTGACAGATCCAGATGCTCCCATCAGG
AAGGACCCCAAATACAGGGAATGGCACCATTTTCTGGTGGTCAACATGAAGACCAACGACATTAGCAGTGGCACAGTCCT
TTCCGATTATGTCGGCTCTGGGCCTCCCAAGGGCACAGGCCTTCATTGATACATCTGGCTGGTATACGAGCAGAGTGGGC
CACTGAAGTGTGATGAGCCCATTCTCAGCAACCCATCTGGAGACCACCGTGGCAAATTCAAAGTGGCATCTTTTCGCAAA
AGG

Alignment

ORF - retro_cfam_526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.68 %
• Parental protein coverage: 80.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGSVMPVDLGKWSGPLSLQEVEERPQHALHVKYTGTEVDELGKVLTPTQVKNRPTSIAWDGLDPGKLYTL
          L.SVM.VDLGKWS.PLSLQEVEE.PQHALHVK.TG.EVDELGKVL.P.QVKNRPTSIAWDGLDPGKL.TL
Retrocopy LRSVMSVDLGKWSRPLSLQEVEEQPQHALHVKHTGMEVDELGKVLMPAQVKNRPTSIAWDGLDPGKLHTL

Parental  VLTDPDAPSRKDPKYREWHHFLVVNMKGNDISSGTVLSDYVGSGPPKGTGLHRYVWLVYEQSGPLKCDEP
          VLTDPDAP.RKDPKYREWHHFLVVNMK.NDISSGTVLSDYVGSGPPKGTGLH.Y.WLVYEQSGPLKCDEP
Retrocopy VLTDPDAPIRKDPKYREWHHFLVVNMKTNDISSGTVLSDYVGSGPPKGTGLH*YIWLVYEQSGPLKCDEP

Parental  ILSNRSGDHRGKFKVASFRKK
          ILSN.SGDHRGKFKVASFRK.
Retrocopy ILSNPSGDHRGKFKVASFRKR

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	0.13 RPM	257.28 RPM
SRP017611_brain	0.24 RPM	340.04 RPM
SRP017611_kidney	0.26 RPM	358.12 RPM
SRP017611_liver	0.07 RPM	146.84 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_526 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_526 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_526 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016143	2 retrocopies	retro_amel_1355, retro_amel_754,
Canis familiaris	ENSCAFG00000009910	1 retrocopy	retro_cfam_526 ,
Callithrix jacchus	ENSCJAG00000009314	2 retrocopies	retro_cjac_1410, retro_cjac_818,
Felis catus	ENSFCAG00000002277	3 retrocopies	retro_fcat_1317, retro_fcat_1360, retro_fcat_299,
Homo sapiens	ENSG00000089220	3 retrocopies	retro_hsap_1456, retro_hsap_2288, retro_hsap_492,
Gorilla gorilla	ENSGGOG00000013281	3 retrocopies	retro_ggor_1121, retro_ggor_1701, retro_ggor_461,
Myotis lucifugus	ENSMLUG00000002259	7 retrocopies	retro_mluc_103, retro_mluc_1612, retro_mluc_1742, retro_mluc_2357, retro_mluc_2373, retro_mluc_984, retro_mluc_998,
Macaca mulatta	ENSMMUG00000005098	4 retrocopies	retro_mmul_1621, retro_mmul_2272, retro_mmul_328, retro_mmul_442,
Mustela putorius furo	ENSMPUG00000002861	3 retrocopies	retro_mputfur_1228, retro_mputfur_1361, retro_mputfur_223,
Mus musculus	ENSMUSG00000032959	4 retrocopies	retro_mmus_138, retro_mmus_1857, retro_mmus_2314, retro_mmus_542,
Nomascus leucogenys	ENSNLEG00000000322	1 retrocopy	retro_nleu_1966,
Oryctolagus cuniculus	ENSOCUG00000008395	2 retrocopies	retro_ocun_1329, retro_ocun_1900,
Otolemur garnettii	ENSOGAG00000001740	1 retrocopy	retro_ogar_2750,
Pongo abelii	ENSPPYG00000005011	2 retrocopies	retro_pabe_1202, retro_pabe_241,
Pan troglodytes	ENSPTRG00000005512	3 retrocopies	retro_ptro_1621, retro_ptro_371, retro_ptro_992,
Rattus norvegicus	ENSRNOG00000001136	3 retrocopies	retro_rnor_1223, retro_rnor_46, retro_rnor_541,
Ictidomys tridecemlineatus	ENSSTOG00000004085	2 retrocopies	retro_itri_1603, retro_itri_961,
Tupaia belangeri	ENSTBEG00000000177	2 retrocopies	retro_tbel_272, retro_tbel_2728,