RetrogeneDB ID: retro_cfam_1201

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 26:33138826..33139370(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CA5B
• Ensembl ID: ENSCAFG00000012150
• Aliases: None
• Description: carbonic anhydrase VB, mitochondrial [Source:HGNC Symbol;Acc:1378]

Sequence

>retro_cfam_1201
ATCGATGCTTGGGGCTCTGAGCATACTGTGGACAGCAAATGTTACCCGGCAGAGCTGCACTTGGTGCATTGGAATGCAGT
CAAATTTGAAAACTTTGAGGATGCAGCACTAGAAGAACATGGTTTGGCTGTAATAGTATTTTTAAAGTTAGGCAAACATC
ACCAAGAACTACAGAAATCGGTGGATACCTTGCCATCAGTCAAGCATAAGGACACCCTTGTGGCATTTGGGTCATTCGAT
CCTTCCTGCCTGATGCCTGCCTGCCCAGATTACTGGACCTACTCGGGGTCCCTGACTACCCCTCCACTCTCTGAGTCTGT
CACCTGGATCATTAAGAAGCAGCCCATAGAGGTTGATCATGATCAGCTTGAGCAGTTTCGGACTCTGCTTTTCACATCAG
AGGGGGAGAAGGAGAAAAGAATGGTGGACAATTTCCACCCCCTCCAGCCCCTGATGAATCGCACTGTCCGCTCTTCCTTC
CGTCATGATTATGTACTGAATAATACAAGCGAAACCCCAGTCTTCAACTAGCCAAGTGACCCCC

Alignment

ORF - retro_cfam_1201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.17 %
• Parental protein coverage: 57.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDAWGSEHTVDSKCYPAELHLVHWNAVKFENFEDAALEEHGLAVIGVFLKLGKHHQELQKLVDTLPSIKH
          IDAWGSEHTVDSKCYPAELHLVHWNAVKFENFEDAALEEHGLAVI.VFLKLGKHHQELQK.VDTLPS.KH
Retrocopy IDAWGSEHTVDSKCYPAELHLVHWNAVKFENFEDAALEEHGLAVI-VFLKLGKHHQELQKSVDTLPSVKH

Parental  KDTLVEFGSFDPSCLMPACPDYWTYSGSLTTPPLSESVTWIIKKQPVEVDHDQLEQFRTLLFTSEGEKEK
          KDTLV.FGSFDPSCLMPACPDYWTYSGSLTTPPLSESVTWIIKKQP.EVDHDQLEQFRTLLFTSEGEKEK
Retrocopy KDTLVAFGSFDPSCLMPACPDYWTYSGSLTTPPLSESVTWIIKKQPIEVDHDQLEQFRTLLFTSEGEKEK

Parental  RMVDNFRPLQPLMNRTVRSSFRHDYVLN-IQAKPQSSTSQVTP
          RMVDNF.PLQPLMNRTVRSSFRHDYVLN.IQAKPQSSTSQVTP
Retrocopy RMVDNFHPLQPLMNRTVRSSFRHDYVLN>IQAKPQSSTSQVTP

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	1.47 RPM
SRP017611_brain	0.16 RPM	1.59 RPM
SRP017611_kidney	0.00 RPM	2.77 RPM
SRP017611_liver	0.00 RPM	0.15 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1201 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1201 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1201 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012150	1 retrocopy	retro_cfam_1201 ,
Callithrix jacchus	ENSCJAG00000004353	1 retrocopy	retro_cjac_2712,