RetrogeneDB ID: retro_cfam_2138

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:23585376..23585683(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP30L
• Ensembl ID: ENSCAFG00000017642
• Aliases: None
• Description: SAP30-like [Source:HGNC Symbol;Acc:25663]

Sequence

>retro_cfam_2138
ATCCAGAGTGTATTAAATAAAAGGAAGAGGAAGACGAGTGACAGTGATGAAAATTCTGAGCACGATACTGACATTCCTGA
GGTTGATCTGTTTCGGCTGCAGGTGAACACTCTATGACACCTTCAATGACACTTATAAATTCCAGACTGGCCTGGGCTTC
CATGTGGCCCGATTAGCAGAAACTGTTGGCTGACACTTCTTGAACGTAACTGTGAGTGAAAAAGAGGCCCTTGCCTACTT
AATCTACATTGTAAAGAGTAATAGGAGTAGAATGGACCAGAAATTGAAGAGCAGCAGGCAGCTTGAG

Alignment

ORF - retro_cfam_2138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.35 %
• Parental protein coverage: 56.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IQSVRNKRKRKTSDDGGDSPEHDTDIPEVDLFQLQVNTLRRYKRH-YKLQTRPGFNKAQLAETVSRHFRN
          IQSV.NKRKRKTSD....S.EHDTDIPEVDLF.LQVNTL.....H.YK.QT..GF..A.LAETV..HF.N
Retrocopy IQSVLNKRKRKTSDSDENS-EHDTDIPEVDLFRLQVNTL*HLQ*H>YKFQTGLGFHVARLAETVG*HFLN

Parental  IPVNEKETLAYFIYMVKSNKSRLDQKSEGGKQLE
          ..V.EKE.LAY.IY.VKSN.SR.DQK.....QLE
Retrocopy VTVSEKEALAYLIYIVKSNRSRMDQKLKSSRQLE

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	4.54 RPM
SRP017611_brain	0.00 RPM	3.81 RPM
SRP017611_kidney	0.00 RPM	4.36 RPM
SRP017611_liver	0.00 RPM	5.08 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2138 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2138 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2138 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016695	1 retrocopy	retro_amel_588,
Bos taurus	ENSBTAG00000004000	1 retrocopy	retro_btau_1024,
Canis familiaris	ENSCAFG00000017642	1 retrocopy	retro_cfam_2138 ,
Felis catus	ENSFCAG00000014985	1 retrocopy	retro_fcat_1968,
Mustela putorius furo	ENSMPUG00000013575	1 retrocopy	retro_mputfur_955,
Ochotona princeps	ENSOPRG00000014552	2 retrocopies	retro_opri_176, retro_opri_953,