RetrogeneDB ID: retro_cfam_1174

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 25:6073287..6073509(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000006265
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SHFM1
• Ensembl ID: ENSCAFG00000002179
• Aliases: None
• Description: split hand/foot malformation (ectrodactyly) type 1 [Source:HGNC Symbol;Acc:10845]

Sequence

>retro_cfam_1174
CAGAGCGTCACCATGTCAGAGAAGAAGCAGCCGGTAGATTTGGGTCTCCTGGAGGAAGACGACGAGTTCGAGGAGTTCCC
TGGCGAAGACTGGGCTGGTTTAGATGAAGATGAAGATGCACATGTCTGGGAGGATAATTGGGATGATGACAATGAAGAGG
ATGACTTCTCTAATCAGTTACGAGCTGAACTAGAGAAACATGGTTATATGATGGAGACCTCA

Alignment

ORF - retro_cfam_1174 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.24 %
• Parental protein coverage: 75.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSVAMSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAELEKHGYK
          .SV.MSEKKQPVDLGLLEEDDEFEEFP.EDWAGLDEDEDAHVWEDNWDDDN.EDDFSNQLRAELEKHGY.
Retrocopy QSVTMSEKKQPVDLGLLEEDDEFEEFPGEDWAGLDEDEDAHVWEDNWDDDNEEDDFSNQLRAELEKHGYM

Parental  METS
          METS
Retrocopy METS

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	0.34 RPM	33.64 RPM
SRP017611_brain	0.16 RPM	12.23 RPM
SRP017611_kidney	1.12 RPM	68.48 RPM
SRP017611_liver	0.00 RPM	12.40 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1174 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1174 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1174 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002179	1 retrocopy	retro_cfam_1174 ,
Cavia porcellus	ENSCPOG00000010402	1 retrocopy	retro_cpor_446,
Echinops telfairi	ENSETEG00000019778	1 retrocopy	retro_etel_961,
Felis catus	ENSFCAG00000023254	2 retrocopies	retro_fcat_1138, retro_fcat_121,
Myotis lucifugus	ENSMLUG00000014208	1 retrocopy	retro_mluc_948,
Oryctolagus cuniculus	ENSOCUG00000026246	3 retrocopies	retro_ocun_1324, retro_ocun_452, retro_ocun_77,