RetrogeneDB ID: retro_cfam_52

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:51797327..51798632(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000016649
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008701
• Aliases: None
• Description: None

Sequence

>retro_cfam_52
ACAAAAGAGGAGGATGTGACTCGGCAGGAGAAGATGGCGACCGTGTGGGATGAGGCTGAGCAAGATGGAATCGGGGAGGA
GGTGCTCAAGATGTCCACAGAAGAGATTATCCAGCGCACACGGCTGCTGGACAGTGAGATCAAGATCATGAAGAGTGAAG
TGTTGCGAGTTACCCATGAACTTCAGGCCATGAAAGACAAGATCAAAGAGAACAGTGAGAAAATCAAAGTGAACAAGACC
TTGCCATATCTTGTCTCCAACGTCATCGAGCTTTTAGATGTTCATCCCAATGACCAAGAAGAGGATGGTGCCAATATTGA
CCTGGATTCTCAGAGGAAGGGTAAATGTGCAGTGATCAAAACCTCTACACGACAGACATACTTCTTGCCTGTGATTGGGT
TGGTGGATGCTGAAAAGCTAAAGCCAGGAGATTTGGTGGGTGTGAACAAAGACTCCTATCTGATCCTGGAGACCCTGCCC
ACAGAGTATGACTCACGGGTGAAGGCCATGGAGGTGGATGAGAGGCCCACGGAACAATATAGTGACATCGGGGGCCTGGA
TAAGCAGATTCAGGAGCTGGTGGAGGCTATTGTCTTGCCAATGAACCACAAGGAGAAGTTCGAGAACTTGGGGATCCAGC
CTCCAAAAGGGGTGTTGATGTATGGCCCCCCAGGTACAGGGAAGACGCTGCTGGCCCGGGCTTGCGCTGCACAAACCAAG
GCTACCTTCCTGAAGCTGGCTGGCCCCCAGCTGGTGCAGATGTTCATTGGGGATGGTGCCAAGCTGGTCCGGGATGCCTT
TGCCCTGGCCAAGGAGAAAGCGCCATCCATTATCTTCATTGATGAGCTGGATGCCACTGGCACTAAGCGCTTTGACAGTG
AGAAGGCCGGAGATCGGGAGGTGCAGAGGACAATGTTGGAGCTTCTGAACCAGCTGGATGGGTTCCAACCCAACACTCAA
GTAAAGGTCATTGCAGCCACCAACAGGGTGGACATCCTCGACCCTGCACTGCTCCGCTCAGGCCGTCTGGACCAGAAGAT
TGAATTCCCAATGCCCAACGAGGAGGCCCGGGCCAGAATCATGCAGATCCACTCCCGCAAGATGAATGTCAGTCCTGATG
TGAACTACGAGGAGCTGGCCCGCTGTATGGATGACTTCAATGGGGCCCAGTGCAAGGCCGTGTGTGTGGAGGCGGGCATG
ATCGCGCTGCGCAGGGGTACCACGGAGCTCACGCATGAGGACTACATGGAAGGCATCCTAGAGGTGCAGGCCAAGAAGAA
AGCCAACCTGCAGTACTACGCCTAG

Alignment

ORF - retro_cfam_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.15 %
• Parental protein coverage: 98.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  REDPVTRQEKMATVWDEAEQDGIGEEVLKMSTEEIIQRTRLLDSEIKIMKSEVLRVTHELQAMKDKIKEN
          .E..VTRQEKMATVWDEAEQDGIGEEVLKMSTEEIIQRTRLLDSEIKIMKSEVLRVTHELQAMKDKIKEN
Retrocopy KEEDVTRQEKMATVWDEAEQDGIGEEVLKMSTEEIIQRTRLLDSEIKIMKSEVLRVTHELQAMKDKIKEN

Parental  SEKIKVNKTLPYLVSNVIELLDVDPNDQEEDGANIDLDSQRKGKCAVIKTSTRQTYFLPVIGLVDAEKLK
          SEKIKVNKTLPYLVSNVIELLDV.PNDQEEDGANIDLDSQRKGKCAVIKTSTRQTYFLPVIGLVDAEKLK
Retrocopy SEKIKVNKTLPYLVSNVIELLDVHPNDQEEDGANIDLDSQRKGKCAVIKTSTRQTYFLPVIGLVDAEKLK

Parental  PGDLVGVNKDSYLILETLPTEYDSRVKAMEVDERPTEQYSDIGGLDKQIQELVEAIVLPMNHKEKFENLG
          PGDLVGVNKDSYLILETLPTEYDSRVKAMEVDERPTEQYSDIGGLDKQIQELVEAIVLPMNHKEKFENLG
Retrocopy PGDLVGVNKDSYLILETLPTEYDSRVKAMEVDERPTEQYSDIGGLDKQIQELVEAIVLPMNHKEKFENLG

Parental  IQPPKGVLMYGPPGTGKTLLARACAAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPSIIFID
          IQPPKGVLMYGPPGTGKTLLARACAAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPSIIFID
Retrocopy IQPPKGVLMYGPPGTGKTLLARACAAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPSIIFID

Parental  ELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSGRLDRKIEFPM
          ELDA.GTKRFDSEKAGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSGRLD.KIEFPM
Retrocopy ELDATGTKRFDSEKAGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSGRLDQKIEFPM

Parental  PNEEARARIMQIHSRKMNVSPDVNYEELARCTDDFNGAQCKAVCVEAGMIALRRGATELTHEDYMEGILE
          PNEEARARIMQIHSRKMNVSPDVNYEELARC.DDFNGAQCKAVCVEAGMIALRRG.TELTHEDYMEGILE
Retrocopy PNEEARARIMQIHSRKMNVSPDVNYEELARCMDDFNGAQCKAVCVEAGMIALRRGTTELTHEDYMEGILE

Parental  VQAKKKANLQYYA
          VQAKKKANLQYYA
Retrocopy VQAKKKANLQYYA

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	66.11 RPM
SRP017611_brain	0.87 RPM	53.19 RPM
SRP017611_kidney	2.11 RPM	85.85 RPM
SRP017611_liver	0.00 RPM	32.99 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_52 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_52 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_52 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008701	1 retrocopy	retro_cfam_52 ,
Monodelphis domestica	ENSMODG00000019911	2 retrocopies	retro_mdom_1035, retro_mdom_1540,
Mustela putorius furo	ENSMPUG00000003992	1 retrocopy	retro_mputfur_1487,