RetrogeneDB ID: retro_cfam_183

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 37:11891125..11891863(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000012558
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000011328
• Aliases: None
• Description: None

Sequence

>retro_cfam_183
ATGAACAACAAGTTCAACACATTGAAAGATGATGACAGTGGGGGCCATGATCAGAATGAAGAAAACAGCACACAGAAAGA
TGGTGAGAAGGAAAAAACGGAACGAGACAAAAGTCAGGGCAGCAGTAACAGGAAGGCTGTTGTCCCTGGGCCAGCAGAGC
ATCCCCTGCAGTACAACTATACTTTCTGGTACTCCAGAAGAACCCCCGGCCGTCCCACCAGCTCACAGAGCTATGAACAG
AATATCAAACAGATCGGCACCTTTGCCTCTGTGGAGCAGTTCTGGAGGTTTTATAGCCACATGGTACGTCCTGGGGACCT
GACAGGCCACAGTGACTTCCATCTCTTCAAAGAAGGAATTAAGCCCATGTGGGAGGATGATGCAAATAAAAATGGTGGCA
AGTGGATTATTCGACTGCGGAAGGGCTTGGCATCCCGTTGCTGGGAGAATCTCATCCTGGCCATGTTGGGGGAACAGTTC
ATGGTTGGGGAGGAGATCTGTGGGGCTGTGGTCTCTGTCCGGTTTCAGGAGGACATTATTTCAATATGGAATAAGACTGC
CAGTGACCAAGCAACCACAGCCCTCATCCGGGATACCCTTCGGCGAGTGCTTAACCTACCTCCCAACACCATTATGGAGT
ACAAAACCCACACCTACAGCATCAAAATGCCAGGCAGGCTGGGCCCCCAAAGGTTCCTTTTTCAAAACCTCTGGAAGCCG
CAGTTGAATGTGCCATGA

Alignment

ORF - retro_cfam_183 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.14 %
• Parental protein coverage: 94.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKDDDSGDHDQNEENSTQKDGEKEKTERDKSQGSSKRKAVVPGPAEHPLQYNYTFWYSRRTPGRPTSSQS
          LKDDDSG.HDQNEENSTQKDGEKEKTERDKSQGSS.RKAVVPGPAEHPLQYNYTFWYSRRTPGRPTSSQS
Retrocopy LKDDDSGGHDQNEENSTQKDGEKEKTERDKSQGSSNRKAVVPGPAEHPLQYNYTFWYSRRTPGRPTSSQS

Parental  YEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLRKGLASRC
          YEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLRKGLASRC
Retrocopy YEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLRKGLASRC

Parental  WENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLPPNTIMEYKTH
          WENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTA.IRDTLRRVLNLPPNTIMEYKTH
Retrocopy WENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTALIRDTLRRVLNLPPNTIMEYKTH

Parental  TDSIK
          T.SIK
Retrocopy TYSIK

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	0.08 RPM	10.96 RPM
SRP017611_brain	0.00 RPM	3.18 RPM
SRP017611_kidney	0.26 RPM	7.53 RPM
SRP017611_liver	0.00 RPM	1.89 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_183 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_183 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_183 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016456	1 retrocopy	retro_amel_1304,
Bos taurus	ENSBTAG00000010598	2 retrocopies	retro_btau_1232, retro_btau_1498,
Canis familiaris	ENSCAFG00000010307	1 retrocopy	retro_cfam_1276,
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183 ,
Choloepus hoffmanni	ENSCHOG00000013109	3 retrocopies	retro_chof_1963, retro_chof_369, retro_chof_567,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717,
Dasypus novemcinctus	ENSDNOG00000016877	1 retrocopy	retro_dnov_1374,
Equus caballus	ENSECAG00000020187	2 retrocopies	retro_ecab_300, retro_ecab_847,
Erinaceus europaeus	ENSEEUG00000015153	2 retrocopies	retro_eeur_57, retro_eeur_668,
Echinops telfairi	ENSETEG00000007930	1 retrocopy	retro_etel_1385,
Homo sapiens	ENSG00000135930	1 retrocopy	retro_hsap_2689,
Macropus eugenii	ENSMEUG00000015519	2 retrocopies	retro_meug_445, retro_meug_644,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Monodelphis domestica	ENSMODG00000002680	1 retrocopy	retro_mdom_1717,
Mustela putorius furo	ENSMPUG00000005206	2 retrocopies	retro_mputfur_110, retro_mputfur_1554,
Nomascus leucogenys	ENSNLEG00000014333	1 retrocopy	retro_nleu_1189,
Otolemur garnettii	ENSOGAG00000009155	1 retrocopy	retro_ogar_104,
Pan troglodytes	ENSPTRG00000013043	1 retrocopy	retro_ptro_1816,
Pteropus vampyrus	ENSPVAG00000007494	4 retrocopies	retro_pvam_1147, retro_pvam_340, retro_pvam_541, retro_pvam_720,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,
Ictidomys tridecemlineatus	ENSSTOG00000003508	3 retrocopies	retro_itri_1270, retro_itri_1370, retro_itri_573,
Tupaia belangeri	ENSTBEG00000004455	11 retrocopies	retro_tbel_1299, retro_tbel_2197, retro_tbel_2623, retro_tbel_2680, retro_tbel_3932, retro_tbel_4471, retro_tbel_4622, retro_tbel_536, retro_tbel_616, retro_tbel_650, retro_tbel_714,
Tursiops truncatus	ENSTTRG00000010927	2 retrocopies	retro_ttru_1799, retro_ttru_1920,