RetrogeneDB ID: retro_cfam_176

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:7762199..7763705(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000000683
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000003222
• Aliases: None
• Description: None

Sequence

>retro_cfam_176
ATGGAGACGATCCTGGAGCAGCAGCGGCGGTACCATGAGGAGAAGGAGCGGCTCATGGACGTCATGGCCAAAGAGATGCT
CACTAAGAAGTCCACGCTCCGGGACCAGATCAATTCCGACCACCGCACACGGGCCATGCAGGATAGATATATGGAAGTGA
GTGGGAACCTGCGGGATTTGTATGATGATAAGGATGGGTTACGAAAGGAGGAACTCAATGCCATTTCAGGACCCAATGAA
TTTGCTGAATTTTATAATAGACTCAAGCAAATAAAAGAATTCCATCGGAAACACCCAAATGAGATCTGTGTGCCAATGTC
AGTGGAATTTGAGGAGCTTCTGAAAGCTCGAGAGAATCCAAGTGAAGAGGCACAAAACTTGGTGGAGTTCACAGATGAAG
AGGGATATGGTCGTTACCTCGACCTCCATGACTGTTACCTCAAATATATTAATCTCAAGGCCTCAGAGAAACTGGATTAT
ATTACCTATCTGTCTATCTTCGACCAGTTATTTGACATTCCTAAAGAGAGGAAAAATGCTGAATATAAGAGATACCTGGA
GATGCTGCTTGAGTACCTTCAAGATTACACAGATCGAGTCAAGCCCCTCCAAGATCAGAACGAACTTTTTGGGAAGATTC
AGAATGAATTTGAGAAGAAGTGGGAGAATGGTACCTTTCCTGGATGGCCGAAAGAGACAAGCAGTGCCCTGACCCATGCT
GGAGCCCATCTTGACCTGTCTGCATTCTCTTCTTGGGAGGAGTTGGCCTCCCTGGGTCTGGACAGATTGAAATCTGCACT
CTTAGCTCTAGGCTTGAAGTGTGGTGGGACCCTAGAAGAGCGAGCCCAGAGGCTCTTCAGCACCAAAGGAAAGTCCCTGG
AGTCACTTGACACCTCCCTGTTTGCCAAAAATCCCAAGTCAAAAGGCACCAAGCGAGACACTGAGAGGAACAAAGACATT
GCCTTCCTAGAAGCCCAAATCTATGAATATGTAGAGATTCTTGGGGAACAGCGGCATCTCACACATGAAAATGTACAACG
CAAGCAGGCGAGGACAGGGGAGGAACGAGAAGAAGAAGAGGAAGAGCAGATCAGTGAGAGTGAAAGTGAAGATGAGGAGA
ATGAGATCATTTACAACCCCAAAAACCTGCCCCTCGGCTGGGATGGCAAACCTATTCCCTACTGGCTGTACAAGCTTCAT
GGTCTAAACATCAACTATAACTGTGAGATTTGTGGAAATTACACGTACCGAGGTCCCAAGGCCTTCCAGCGGCACTTTGC
TGAGTGGCGTCATGCCCACGGCATGAGGTGTTTGGGCATCCCAAACACTGCCCACTTCGCTAATGTGACACAGATCGAAG
ATGCTGTCTCCTTGTGGGCCAAGCTGAAACTGCAGAAGGCATCAGAGCGATGGCAGCCTGACACCGAGGAAGAATATGAA
GACTCCAGCGGGAACGTGGTGAATAAGAAGACCTATGAGGACCTGAAGAGACAAGGACTGCTCTAG

Alignment

ORF - retro_cfam_176 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDLYDDKDGLRKE
          METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDLYDDKDGLRKE
Retrocopy METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDLYDDKDGLRKE

Parental  ELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKARENPSEEAQNLVEFTDEEGYGRYL
          ELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKARENPSEEAQNLVEFTDEEGYGRYL
Retrocopy ELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKARENPSEEAQNLVEFTDEEGYGRYL

Parental  DLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNAEYKRYLEMLLEYLQDYTDRVKPLQDQNELF
          DLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNAEYKRYLEMLLEYLQDYTDRVKPLQDQNELF
Retrocopy DLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNAEYKRYLEMLLEYLQDYTDRVKPLQDQNELF

Parental  GKIQNEFEKKWENGTFPGWPKETSSALTHAGAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEE
          GKIQNEFEKKWENGTFPGWPKETSSALTHAGAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEE
Retrocopy GKIQNEFEKKWENGTFPGWPKETSSALTHAGAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEE

Parental  RAQRLFSTKGKSLESLDTSLFAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRHLTHENVQRKQA
          RAQRLFSTKGKSLESLDTSLFAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRHLTHENVQRKQA
Retrocopy RAQRLFSTKGKSLESLDTSLFAKNPKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRHLTHENVQRKQA

Parental  RTGEEREEEEEEQISESESEDEENEIIYNPKNLPLGWDGKPIPYWLYKLHGLNINYNCEICGNYTYRGPK
          RTGEEREEEEEEQISESESEDEENEIIYNPKNLPLGWDGKPIPYWLYKLHGLNINYNCEICGNYTYRGPK
Retrocopy RTGEEREEEEEEQISESESEDEENEIIYNPKNLPLGWDGKPIPYWLYKLHGLNINYNCEICGNYTYRGPK

Parental  AFQRHFAEWRHAHGMRCLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYEDSSGNVVNKK
          AFQRHFAEWRHAHGMRCLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYEDSSGNVVNKK
Retrocopy AFQRHFAEWRHAHGMRCLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYEDSSGNVVNKK

Parental  TYEDLKRQGLL
          TYEDLKRQGLL
Retrocopy TYEDLKRQGLL

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	0.17 RPM	18.31 RPM
SRP017611_brain	0.24 RPM	13.58 RPM
SRP017611_kidney	0.33 RPM	19.08 RPM
SRP017611_liver	0.00 RPM	7.32 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_176 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_176 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001262	1 retrocopy	retro_amel_485,
Canis familiaris	ENSCAFG00000003222	1 retrocopy	retro_cfam_176 ,
Callithrix jacchus	ENSCJAG00000002176	1 retrocopy	retro_cjac_4109,
Cavia porcellus	ENSCPOG00000008660	1 retrocopy	retro_cpor_658,
Homo sapiens	ENSG00000183431	2 retrocopies	retro_hsap_2441, retro_hsap_937,
Macropus eugenii	ENSMEUG00000002534	3 retrocopies	retro_meug_1135, retro_meug_1346, retro_meug_642,
Macaca mulatta	ENSMMUG00000023199	1 retrocopy	retro_mmul_631,
Monodelphis domestica	ENSMODG00000017729	1 retrocopy	retro_mdom_269,
Nomascus leucogenys	ENSNLEG00000011720	1 retrocopy	retro_nleu_2775,
Pan troglodytes	ENSPTRG00000000559	2 retrocopies	retro_ptro_1411, retro_ptro_649,
Sorex araneus	ENSSARG00000014204	1 retrocopy	retro_sara_407,