RetrogeneDB ID: retro_cfam_1973

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:15550243..15550922(+)
• Located in intron of: ENSCAFG00000010877

Retrocopy information

• Ensembl ID: ENSCAFG00000010967
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CMSS1
• Ensembl ID: ENSCAFG00000009230
• Aliases: CMSS1, C33H3orf26
• Description: cms1 ribosomal small subunit homolog (yeast) [Source:HGNC Symbol;Acc:28666]

Sequence

>retro_cfam_1973
TGTGGCCTCATCAAGATTTCTGTTTCCACAAAAGAAGATGTCACCAAGACAAGGAGGAGAAGAAAGAAGAAAATTACTGA
TGTTCTTGCAAAATCAGAGCCAAAACCGGGGACCCCTGAAGACCTGCAGAACTTGATGAAGGACTATTTCAGCAGCAGCC
GCTCAGTGATTGAATTAGAAGAACTAAACCTACCAGACTCCTGTTTCCTCAAGGCCAATGATTTGACTCATAGTCTTTCA
TCATACCTAAGAGAAATCTGCCCTAAGTGGGTAAAACTTCGGAAAAACCATAATGAGAAGAAATCGGTTCTGATGCTGAT
CATCTGCAGCTCTGCTGTCCGGGCCTTGGAGCTCATTAGGTCGATGACAGCATTCAGAGGAGACAGCAAAGTTATGAAAT
TATTTGCAAAACACATAAAGGTCCAGGAGCAGGTAAAGCTGCTGGGGAAGCGTGTTGTACACCTGGGTGTAGGAACACCA
GGGAGGATTAAAGAACTCATTAAACAAGGTGGCCTTAATTTGAACCCCTTAAAGTTCCTGGTTTTTGACTGGAACTGGAG
AGATCAGAAGTTGAGGAGGATGATGGACATTCCTGAGATTAGAAAGGAGGTTTTTGAACTTCTGGAAATGGGAGTCCTCA
AGTCTGTGCAAATCAGAATCTTTGAAGCTGGGCCTTTTC

Alignment

ORF - retro_cfam_1973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.48 %
• Parental protein coverage: 81.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CFLIKPK-ETKEDATKTRRRRKKKITDVLAKSEPKPGTPEDLQNLMKDYFSSSRSVIELEELNLPDSCFL
          C.LIK....TKED.TKTRRRRKKKITDVLAKSEPKPGTPEDLQNLMKDYFSSSRSVIELEELNLPDSCFL
Retrocopy CGLIKISVSTKEDVTKTRRRRKKKITDVLAKSEPKPGTPEDLQNLMKDYFSSSRSVIELEELNLPDSCFL

Parental  KANDLTHSLSSYLREICPKWVKLRKNHNEKKSVLMLIICSSAVRALELIRSMTAFRGDSKVMKLFAKHIK
          KANDLTHSLSSYLREICPKWVKLRKNHNEKKSVLMLIICSSAVRALELIRSMTAFRGDSKVMKLFAKHIK
Retrocopy KANDLTHSLSSYLREICPKWVKLRKNHNEKKSVLMLIICSSAVRALELIRSMTAFRGDSKVMKLFAKHIK

Parental  VQEQVKLLEKRVVHLGVGTPGRIKELIKQGGLNLNPLKFLVFDWNWRDQKLRRMMDIPEIRKEVFELLEM
          VQEQVKLL.KRVVHLGVGTPGRIKELIKQGGLNLNPLKFLVFDWNWRDQKLRRMMDIPEIRKEVFELLEM
Retrocopy VQEQVKLLGKRVVHLGVGTPGRIKELIKQGGLNLNPLKFLVFDWNWRDQKLRRMMDIPEIRKEVFELLEM

Parental  GVL-SLCKSESLKLGLF
          GVL.SLCKSESLKLGLF
Retrocopy GVL>SLCKSESLKLGLF

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	9.62 RPM
SRP017611_brain	0.00 RPM	13.26 RPM
SRP017611_kidney	0.00 RPM	4.49 RPM
SRP017611_liver	0.00 RPM	2.54 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1973 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1973 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1973 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	ENSCAFG00000009230	1 retrocopy	retro_cfam_1973 ,
Mustela putorius furo	ENSMPUG00000011324	2 retrocopies	retro_mputfur_1009, retro_mputfur_783,
Ochotona princeps	ENSOPRG00000002986	1 retrocopy	retro_opri_952,