RetrogeneDB ID: retro_cfam_421

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:38887323..38888178(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000032347
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RRAGB
• Ensembl ID: ENSCAFG00000016503
• Aliases: None
• Description: Ras-related GTP binding B [Source:HGNC Symbol;Acc:19901]

Sequence

>retro_cfam_421
TTTGCGAACTATATCGCTCGCGACACCCGGCGCCTGGGGGCCACCATCGATGTGGAGCACTCCCACGTCCGATTCCTGGG
CAACCTGGTGCTCAACCTGTGGGACTGCGGCGGTCAGGACACCTTCATGGAGAACTACTTCACCAGCCAGCGAGACAACA
TCTTCCGTAACGTGGAGGTGCTGATCTACGTGTTTGACGTGGAGAGCCGCGAACTGGAAAAGGACATGCATTATTACCAG
TCGTGTCTGGAGGCCATCCTCCAGAACTCTCCGGATGCCAAAATCTTCTGCCTGGTGCACAAAATGGATCTGGTTCAGGA
GGATCAGCGTGACCTGATTTTTAAAGAGCGAGAGGAAGACCTGCGGCGTCTGTCTCGCCCCCTGGAATGCGCTTGTTTTC
GAACCTCCATCTGGGACGAAACGCTCTACAAAGCCTGGTCCAGTATTGTCTACCAGCTCATTCCCAATGTGCAGCAGCTG
GAGATGAACCTCAGGAATTTTGCCCAAATTATTGAGGCCGACGAAGTCCTGCTGTTCGAGAGGGCTACGTTCTTGGTCAT
TTCCCATTACCAGTGCAAGGAGCAGCGTGATGTCCACCGGTTCGAGAAGATCAGCAACATCATTAAGCAGTTCAAGCTGA
GCTGCAGTAAATTAGCCGCTTCTTTCCAGAGCATGGAAGTTCGAAATTCTAACTTCGCGGCCTTCATCGACATCTTCACC
TCAAACACGTACGTGATGGTGGTTATGTCTGACCCGTCGATCCCTTCCGCAGCTACTCTGATCAACATTCGCAATGCCAG
GAAACACTTTGAGAAGCTGGAGAGAGTGGATGGCCCCAAGCACAGCCTCCTGATG

Alignment

ORF - retro_cfam_421 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.39 %
• Parental protein coverage: 76.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FSTYSLVDSVGNTKTFDVEHSHVRFLGNLVLNLWDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESR
          F..Y...D......T.DVEHSHVRFLGNLVLNLWDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESR
Retrocopy FANYIARDTRRLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESR

Parental  ELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDE
          ELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDE
Retrocopy ELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDE

Parental  TLYKAWSSIVYQLIPNVQQLEMNLRNFAEIIEADEVLLFERATFLVISHYQCKEQRDAHRFEKISNIIKQ
          TLYKAWSSIVYQLIPNVQQLEMNLRNFA.IIEADEVLLFERATFLVISHYQCKEQRD.HRFEKISNIIKQ
Retrocopy TLYKAWSSIVYQLIPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQ

Parental  FKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPK
          FKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPK
Retrocopy FKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPK

Parental  QCLLM
          ..LLM
Retrocopy HSLLM

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	42.08 RPM	15.83 RPM
SRP017611_brain	55.81 RPM	10.72 RPM
SRP017611_kidney	51.05 RPM	2.91 RPM
SRP017611_liver	22.77 RPM	1.31 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cfam_421 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
GR892675	38887683	38887954	97.8	265	6	259

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_421 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_421 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4
Pan troglodytes	retro_ptro_48
Pongo abelii	retro_pabe_191
Macaca mulatta	retro_mmul_249
Callithrix jacchus	retro_cjac_117
Mus musculus	retro_mmus_159
Sus scrofa	retro_sscr_15
Equus caballus	retro_ecab_608

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012920	1 retrocopy	retro_amel_1842,
Canis familiaris	ENSCAFG00000016503	1 retrocopy	retro_cfam_421 ,
Callithrix jacchus	ENSCJAG00000007317	1 retrocopy	retro_cjac_117,
Cavia porcellus	ENSCPOG00000011266	1 retrocopy	retro_cpor_86,
Equus caballus	ENSECAG00000006020	1 retrocopy	retro_ecab_608,
Felis catus	ENSFCAG00000013932	1 retrocopy	retro_fcat_21,
Homo sapiens	ENSG00000083750	1 retrocopy	retro_hsap_4,
Gorilla gorilla	ENSGGOG00000011501	1 retrocopy	retro_ggor_65,
Loxodonta africana	ENSLAFG00000016144	1 retrocopy	retro_lafr_102,
Myotis lucifugus	ENSMLUG00000015720	1 retrocopy	retro_mluc_40,
Macaca mulatta	ENSMMUG00000017635	1 retrocopy	retro_mmul_249,
Mustela putorius furo	ENSMPUG00000003730	1 retrocopy	retro_mputfur_87,
Mus musculus	ENSMUSG00000041658	1 retrocopy	retro_mmus_159,
Nomascus leucogenys	ENSNLEG00000016350	1 retrocopy	retro_nleu_13,
Oryctolagus cuniculus	ENSOCUG00000008666	1 retrocopy	retro_ocun_166,
Otolemur garnettii	ENSOGAG00000000345	1 retrocopy	retro_ogar_675,
Procavia capensis	ENSPCAG00000003417	1 retrocopy	retro_pcap_6,
Pongo abelii	ENSPPYG00000020398	1 retrocopy	retro_pabe_191,
Pan troglodytes	ENSPTRG00000021955	1 retrocopy	retro_ptro_48,
Rattus norvegicus	ENSRNOG00000003160	1 retrocopy	retro_rnor_2,
Sus scrofa	ENSSSCG00000029800	1 retrocopy	retro_sscr_15,