RetrogeneDB ID: retro_cfam_1067

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:16501343..16502003(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000004920
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000018826
• Aliases: None
• Description: None

Sequence

>retro_cfam_1067
TCTGACATTTGGTCATTGGGAATTATTATTGAACTAGCCAAGGGAGGACCACCTAACTCTGGTATGCATCCAGTGAGAGT
TCTGTTATCTTAATCCAAGAAAACAATCTTCCAACTCTTGTTGGAGACTTCACTAAGTACTTTAAGGGGTTTATTGATGC
AAGCATCAACAAAGATCCATCATTTCGTCCTACAGCTAAAGAATTTCTGAAACACAAATTCATTGTAAAAAAAAAAAAAA
ATCCAAAGAAGACTTCTTATCTGATGGAACTGATAGATCGATTTAAGAGCTGGAAAGCAGAAGGGCACAGGGATGATGAA
ATTGATTCTGAGGGCTCTAATTCGGAAGCCACCAGCAGAGAAAACAACACTGATCCCGAATGGAGCTTTACCACCGTATT
AAAGAAAGCCCAATCCAAGGAAACCCCAGAAAGGGGCAGAGCAAGATCATGTGCAAACCCTGACCTGTTTGTCTATGATA
ATCACACCTGCATTTGCTGAACTTAAACAGCAGGATGAGAATAACGCTAGCAGGAATCAGGCAATTGAAGAACTCGAGAA
AAGTATTGCTGGGACAGAAGCCGCTTGGCCTGGCATCACAGATAAAATGGTGAGGAAATTAATTGAAAAATTTTGCAAGT
GTCCACCCAATGAAACCCCC

Alignment

ORF - retro_cfam_1067 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.54 %
• Parental protein coverage: 52.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ADIWSLGITAIELAKGEPPNSDMHPMRVL-FLIPK-NNPPTLVGDFTKSFKEFIDACLNKDPSFRPTAKE
          .DIWSLGI..IELAKG.PPNS.MHP.RVL..L.P..NN.PTLVGDFTK.FK.FIDA..NKDPSFRPTAKE
Retrocopy SDIWSLGII-IELAKGGPPNSGMHPVRVL>YLNPR>NNLPTLVGDFTKYFKGFIDASINKDPSFRPTAKE

Parental  LLKHKFIVKNSKKTSYLTELIDRFKR---WKAEGHSDDESDSEGSDSESTSRENNTHPEWSFTTVRK-KP
          .LKHKFI............L.....R...WKAEGH.DDE.DSEGS.SE.TSRENNT.PEWSFTTV.K.KP
Retrocopy FLKHKFIXXXXXXPKKTSYLMELIDRFKSWKAEGHRDDEIDSEGSNSEATSRENNTDPEWSFTTVLK>KP

Parental  DPKKLQNGAEQDLVQTLSCLSMIITPAFAELKQQDENNASRNQAIEELEKSIAVAEAACPGITDKMVKKL
          .P.K.Q.GAEQD.VQTL.CLSMIITPAFAELKQQDENNASRNQAIEELEKSIA..EAA.PGITDKMV.KL
Retrocopy NPRKPQKGAEQDHVQTLTCLSMIITPAFAELKQQDENNASRNQAIEELEKSIAGTEAAWPGITDKMVRKL

Parental  IEKFQKCSADESP
          IEKF.KC...E.P
Retrocopy IEKFCKCPPNETP

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	0.00 RPM	8.06 RPM
SRP017611_brain	0.00 RPM	4.60 RPM
SRP017611_kidney	0.00 RPM	3.90 RPM
SRP017611_liver	0.00 RPM	1.09 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1067 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1067 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1067 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018826	1 retrocopy	retro_cfam_1067 ,
Felis catus	ENSFCAG00000026530	1 retrocopy	retro_fcat_223,
Macropus eugenii	ENSMEUG00000013597	1 retrocopy	retro_meug_307,
Microcebus murinus	ENSMICG00000009064	1 retrocopy	retro_mmur_527,
Otolemur garnettii	ENSOGAG00000002621	1 retrocopy	retro_ogar_2658,