RetrogeneDB ID: retro_cfam_1644

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:13351930..13352495(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000012971
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM57A
• Ensembl ID: ENSCAFG00000019129
• Aliases: None
• Description: family with sequence similarity 57, member A [Source:HGNC Symbol;Acc:29646]

Sequence

>retro_cfam_1644
CACTGGCTTGCCCGAGAGTATGTCTGGTTCTTGATTCCGTACATGATCTGTGACTTCTATGCCATGTACCTCTGTGAGTG
GTACCGAACCAGAGACCAGAACCACAGACACTCCCTCACCACTTTTCGAAACTTCCTAAGTAAAAACCACCTCATGGTCA
TGCACCACACAGTCATCCTGTTTGTCCTTGTGCCAGTTTCACAGAGGCTTAGGGGAGACCTTGGAGACTTCTTTGTTGGC
TGCATCTTCATGGCAAAACTGAGCACTCCGTTTGTGTTACTGGGCAGAGTCCTGATTCAGCTAAAGCAGCAGCACACCCT
TCTGTACAAAGTGAACGGAATCCTCATGCTGACCACCTTCCTTTCCTGTCGGATCCTCCTCTTCCCTTTCATGTACAGGT
CTTATGGCCAACAGCAGGGACTCAGCCCACTCTGAGTGCCATTCAGCATCCCTTTACTGCAATGTGGCCAATGCCTTCCT
CATTGCTCCCCAGATCTACTGGTTCTCTCTGCTGTGCAAGAAAGCAACCCGGCTCTTTGACACCGCCCCAGCCAAAAAGG
ATGGC

Alignment

ORF - retro_cfam_1644 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.19 %
• Parental protein coverage: 73.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HWLAREYVWFLIPYMIYDSYAMYLCEWYRTRDQNHRHSLTTFRNFLSKNRLMVAHHAVILFVLVPVAQRL
          HWLAREYVWFLIPYMI.D.YAMYLCEWYRTRDQNHRHSLTTFRNFLSKN.LMV.HH.VILFVLVPV.QRL
Retrocopy HWLAREYVWFLIPYMICDFYAMYLCEWYRTRDQNHRHSLTTFRNFLSKNHLMVMHHTVILFVLVPVSQRL

Parental  RGDLGDFFVGCIFMAELSTPFVSLGRVLIQLKQQHTLLYKVNGILTLTTFLSCRILLFPFMYWSYGQQQG
          RGDLGDFFVGCIFMA.LSTPFV.LGRVLIQLKQQHTLLYKVNGIL.LTTFLSCRILLFPFMY.SYGQQQG
Retrocopy RGDLGDFFVGCIFMAKLSTPFVLLGRVLIQLKQQHTLLYKVNGILMLTTFLSCRILLFPFMYRSYGQQQG

Parental  LSPLRVPFSI-PF-YCNVANAFLIAPQIYWFSLLCKKATRLFDTAPAKKDG
          LSPL.VPFSI.PF.YCNVANAFLIAPQIYWFSLLCKKATRLFDTAPAKKDG
Retrocopy LSPL*VPFSI<PF<YCNVANAFLIAPQIYWFSLLCKKATRLFDTAPAKKDG

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	43.34 RPM
SRP017611_brain	0.00 RPM	12.70 RPM
SRP017611_kidney	0.00 RPM	11.82 RPM
SRP017611_liver	0.00 RPM	6.82 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1644 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1644 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1644 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019129	1 retrocopy	retro_cfam_1644 ,
Echinops telfairi	ENSETEG00000019235	1 retrocopy	retro_etel_7,
Loxodonta africana	ENSLAFG00000017562	1 retrocopy	retro_lafr_518,
Microcebus murinus	ENSMICG00000009347	1 retrocopy	retro_mmur_111,