RetrogeneDB ID: retro_cfam_844

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:19766585..19767428(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000004191
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBM17
• Ensembl ID: ENSCAFG00000005206
• Aliases: None
• Description: RNA binding motif protein 17 [Source:HGNC Symbol;Acc:16944]

Sequence

>retro_cfam_844
GGAGACGTTTTGATGCCTTTAGCTGATGAATACGATCCCATGTCTCCTGACGACTATGAGAAAGTAGTGAAACGCCAAAG
AGAGGAACGACAGAGACAGCGGGAGCTGGAAAGACAAAGAAATAGAAGAGCGAGGAAAGAGGCGTAGAGACGGACAGGAA
GCTAGTGGGTTTTCGAGGCGACCAGATCCAGCTGTGATGAGGCCGAGGATTATGAGCGGGAGAGGCGGAGAAGAAGCATG
GGCGGAGCTGCCATTGCACCACCCACTTCTCTTGTAGAGAAGGACAAAGAGTTGCCCCGAGATTTCCCTTGCGAAGAGGA
TTCCAGACCTCACTCTCCGTCTTCCAAAGCTGCTATCCCCCCTCCAGTGTACGAGGAACAAGACAGCCCCAGATCTCCGC
CTGCACCTGGCAGCTCCTTCCTTGCCAACATGGATGGCACAGGAGCACATAAAATCATGCAGAAGTACCGCTTCCGGGAA
GGCCAGGGTCTTGGGAAGCACCAACAAGGGCTGAGCATAGCACTGTCCGTGGAGAAGACAGGCAAGCGAGGAGGCAAGAT
CATTGTGGGTGATGCCACCGAGAAAGATGCATCCAAGGAGTCAGATTCAAATCCATTAACTGAAATACTTAAGTGTCCTA
CCAAAGTGGTCCTCCTAAGGAGCATGGTTGATGCAGGAGAGGTAGATGAAGACTTGGAAGCAGAAACCAAGGAAGAGTGT
GAACAATACGGCAAAGTTGGAAAATGTGCGATATTTGAAATTCCTGGTGCCCCTGATGATGAAACAGTACGAATATTTTT
AGAGTTTGAGAGAGTTGGGTCAGCAATTAAAGCTGTTGTTGAT

Alignment

ORF - retro_cfam_844 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.92 %
• Parental protein coverage: 70.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GEVLIPLADEYDPMFPNDYEKVVKRQREERQRQRELERQKEIEER-EKRRKDRHEASGFSRRPDP-DSDE
          G.VL.PLADEYDPM.P.DYEKVVKRQREERQRQRELERQ.....R...RR.D..EASGFSRRPDP...DE
Retrocopy GDVLMPLADEYDPMSPDDYEKVVKRQREERQRQRELERQRNRRAR>KRRR-DGQEASGFSRRPDP<SCDE

Parental  DEDYERERRKRSMGGAAIAPPTSLVEKDKELPRDFPYEEDSRPRSQSSKAAIPPPVYEEQDRPRSPTGPG
          .EDYERERR.RSMGGAAIAPPTSLVEKDKELPRDFP.EEDSRP.S.SSKAAIPPPVYEEQD.PRSP..PG
Retrocopy AEDYERERRRRSMGGAAIAPPTSLVEKDKELPRDFPCEEDSRPHSPSSKAAIPPPVYEEQDSPRSPPAPG

Parental  NSFLANMGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSVEKTSKRGGKIIVGDATEKDASKKSDSNPLT
          .SFLANM.GT.AHKIMQKY.FREGQGLGKH.QGLS.ALSVEKT.KRGGKIIVGDATEKDASK.SDSNPLT
Retrocopy SSFLANMDGTGAHKIMQKYRFREGQGLGKHQQGLSIALSVEKTGKRGGKIIVGDATEKDASKESDSNPLT

Parental  EILKCPTKVVLLRNMVGAGEVDEDLEAETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIK
          EILKCPTKVVLLR.MV.AGEVDEDLEAETKEECE.YGKVGKC.IFEIPGAPDDE.VRIFLEFERV.SAIK
Retrocopy EILKCPTKVVLLRSMVDAGEVDEDLEAETKEECEQYGKVGKCAIFEIPGAPDDETVRIFLEFERVGSAIK

Parental  AVVD
          AVVD
Retrocopy AVVD

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	50.65 RPM
SRP017611_brain	0.00 RPM	28.03 RPM
SRP017611_kidney	0.00 RPM	34.93 RPM
SRP017611_liver	0.00 RPM	21.54 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_844 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_844 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_844 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021951	2 retrocopies	retro_btau_1057, retro_btau_530,
Canis familiaris	ENSCAFG00000005206	1 retrocopy	retro_cfam_844 ,
Callithrix jacchus	ENSCJAG00000020573	1 retrocopy	retro_cjac_432,
Equus caballus	ENSECAG00000008939	1 retrocopy	retro_ecab_547,
Erinaceus europaeus	ENSEEUG00000013077	1 retrocopy	retro_eeur_390,
Homo sapiens	ENSG00000134453	1 retrocopy	retro_hsap_1551,
Macropus eugenii	ENSMEUG00000011347	1 retrocopy	retro_meug_438,
Macaca mulatta	ENSMMUG00000015152	2 retrocopies	retro_mmul_1209, retro_mmul_771,
Mus musculus	ENSMUSG00000037197	1 retrocopy	retro_mmus_2855,
Otolemur garnettii	ENSOGAG00000015687	1 retrocopy	retro_ogar_1119,
Pongo abelii	ENSPPYG00000002067	1 retrocopy	retro_pabe_1284,
Pan troglodytes	ENSPTRG00000002265	1 retrocopy	retro_ptro_1044,
Ictidomys tridecemlineatus	ENSSTOG00000013591	1 retrocopy	retro_itri_1376,
Tursiops truncatus	ENSTTRG00000001344	1 retrocopy	retro_ttru_1758,