RetrogeneDB ID: retro_cfam_1939

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:10916790..10917198(-)
• Located in intron of: ENSCAFG00000013144

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS15
• Ensembl ID: ENSCAFG00000030390
• Aliases: None
• Description: mitochondrial ribosomal protein S15 [Source:HGNC Symbol;Acc:14504]

Sequence

>retro_cfam_1939
AAGATCATGGCAAAGTATGTGAGAGTATGTGAGAACACCATTTCCTTGGTGGCTCGAATTGTTGCCTTTAACTGTCAAGC
TCTGCAATTATAAAGGACACATGCACAAATATTGAAAGAACAAGCCCACAAACACTATCCACCGATGAGCATCGATCAGA
GGAAAAACATGCTCAGAAACTCCAGAAGAGTTTTTGGAGCTATAATGTCTTTGAGAAGACATGCAAGGAGCTGGAGATTG
AGTGCACCTTTCCCCTCTGTACTACTGAAAAGCCCACCACTGCTGGTGACCAAGAAGGCTCTGTGCATTTAGGTTTTCCA
GGAGACAAAAGCTGAGAAAGCAGGGAGGGGATAAAAGGCCTTAAAAGCTGAAGCAGAAACCTGGAAACAAGGCCAGAAGA
ATCTAGAG

Alignment

ORF - retro_cfam_1939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.45 %
• Parental protein coverage: 71.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QLMSKIVANPEDTSSLEARIVA-LTVKIRNFEEHMQKHRKDK-VHKRYLLMSIDQRKKLLKN-LRKT--N
          ..M.K.V...E.T.SL.ARIVA.LTVK..N...HM.K..K.K..HK.Y..MSIDQRK..L.N.L.K....
Retrocopy KIMAKYVRVCENTISLVARIVA>LTVKLCNYKGHMHKY*KNK<AHKHYPPMSIDQRKNMLRN<LQKSFWS

Parental  YSVFEKTCKELGIEYTFP-PLYHRKGHQRW-VTKKALCIRVFQE--AQKLKKQKRALKAKAAAQKQGQKN
          Y.VFEKTCKEL.IE.TFP.PLY..K.H..W.VTKKALCI.VFQE..A.K......ALKA.A...KQGQKN
Retrocopy YNVFEKTCKELEIECTFP<PLYY*KAHHCW<VTKKALCI*VFQETKAEKAGRG*KALKAEAETWKQGQKN

Parental  PE
          .E
Retrocopy LE

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	54.26 RPM
SRP017611_brain	0.56 RPM	71.45 RPM
SRP017611_kidney	0.07 RPM	91.13 RPM
SRP017611_liver	0.00 RPM	36.40 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1939 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1939 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1939 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001463	1 retrocopy	retro_amel_1564,
Canis familiaris	ENSCAFG00000030390	1 retrocopy	retro_cfam_1939 ,
Callithrix jacchus	ENSCJAG00000001852	3 retrocopies	retro_cjac_3095, retro_cjac_761, retro_cjac_859,
Cavia porcellus	ENSCPOG00000010877	1 retrocopy	retro_cpor_430,
Dipodomys ordii	ENSDORG00000007581	1 retrocopy	retro_dord_118,
Felis catus	ENSFCAG00000005265	1 retrocopy	retro_fcat_915,
Homo sapiens	ENSG00000116898	1 retrocopy	retro_hsap_1594,
Myotis lucifugus	ENSMLUG00000006475	1 retrocopy	retro_mluc_1945,
Monodelphis domestica	ENSMODG00000017813	1 retrocopy	retro_mdom_1094,
Mus musculus	ENSMUSG00000028861	1 retrocopy	retro_mmus_3447,
Nomascus leucogenys	ENSNLEG00000011467	1 retrocopy	retro_nleu_615,
Otolemur garnettii	ENSOGAG00000002656	2 retrocopies	retro_ogar_1327, retro_ogar_16,
Pongo abelii	ENSPPYG00000001537	1 retrocopy	retro_pabe_1310,
Pan troglodytes	ENSPTRG00000000541	1 retrocopy	retro_ptro_1071,
Sus scrofa	ENSSSCG00000026393	1 retrocopy	retro_sscr_1190,
Ictidomys tridecemlineatus	ENSSTOG00000000608	1 retrocopy	retro_itri_454,
Tupaia belangeri	ENSTBEG00000000958	4 retrocopies	retro_tbel_1633, retro_tbel_4438, retro_tbel_845, retro_tbel_882,
Tarsius syrichta	ENSTSYG00000008948	2 retrocopies	retro_tsyr_1612, retro_tsyr_372,
Tursiops truncatus	ENSTTRG00000002345	1 retrocopy	retro_ttru_1500,