RetrogeneDB ID: retro_cfam_730

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:26248311..26248878(-)
• Located in intron of: ENSCAFG00000005841

Retrocopy information

• Ensembl ID: ENSCAFG00000005837
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EMC3
• Ensembl ID: ENSCAFG00000005202
• Aliases: None
• Description: ER membrane protein complex subunit 3 [Source:HGNC Symbol;Acc:23999]

Sequence

>retro_cfam_730
CACTACGAGTCGATCCTGCTGCAGAGTGACAAGAAGCTCACTCAGGAACAAGTCTCCAACAGTCAAGTCCTAATTCGAAG
CAGAGTCCTCAGGGAAAATGGAAAATACATTCCCAAACAGTCTTTCTTGACACGAAAATATTACTTCAACAACCCAGAGG
ATGGATTTTTCAAAAAAACTAAAAGGAAGGTAGTGCCTCCTTCTCCTATGACTGATCCCACTATGCTCACAGACATGATG
AAAAGCAATGTGACAAATGTTCTCCCTATGATTCTTATTGGTGGCTGGATCAACATGACATTCTCTGGCTTTGTCACAAC
CAAGGTACCATTTCCACTGACTCTCTGTTTTAAGCCTATGCTACAGCAGGGAATTGAACTACTCACATTAGATGCATCCC
GCGTGAGCTCTGCATCCTGGTACTTCCTCAGTGTCTTTGGGCTTCGGAGCATTTACTCTCTGATTCTGGGCCAAGATAAT
GCCGCTGACCAGTCACAGATGATGCAGGAACAGATGACTGGAGCAGCCATGGCCATGCCTGCGGACACCAACAAAGCTTT
CAAGACA

Alignment

ORF - retro_cfam_730 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.77 %
• Parental protein coverage: 84.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HYVSILLQSDKKLTQEQVSDSQVLIRSRVLRENGKYIPKQSFLTRKYYFNNPEDGFFKKTKRKVVPPSPM
          HY.SILLQSDKKLTQEQVS.SQVLIRSRVLRENGKYIPKQSFLTRKYYFNNPEDGFFKKTKRKVVPPSPM
Retrocopy HYESILLQSDKKLTQEQVSNSQVLIRSRVLRENGKYIPKQSFLTRKYYFNNPEDGFFKKTKRKVVPPSPM

Parental  TDPTMLTDMMKGNVTNVLPMILIGGWINMTFSGFVTTKVPFPLTLRFKPMLQQGIELLTLDASWVSSASW
          TDPTMLTDMMK.NVTNVLPMILIGGWINMTFSGFVTTKVPFPLTL.FKPMLQQGIELLTLDAS.VSSASW
Retrocopy TDPTMLTDMMKSNVTNVLPMILIGGWINMTFSGFVTTKVPFPLTLCFKPMLQQGIELLTLDASRVSSASW

Parental  YFLNVFGLRSIYSLILGQDNAADQSRMMQEQMTGAAMAMPADTNKAFKS
          YFL.VFGLRSIYSLILGQDNAADQS.MMQEQMTGAAMAMPADTNKAFK.
Retrocopy YFLSVFGLRSIYSLILGQDNAADQSQMMQEQMTGAAMAMPADTNKAFKT

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	4.96 RPM	46.37 RPM
SRP017611_brain	3.81 RPM	50.65 RPM
SRP017611_kidney	5.68 RPM	66.70 RPM
SRP017611_liver	1.60 RPM	18.93 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_730 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_730 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_730 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005202	1 retrocopy	retro_cfam_730 ,
Callithrix jacchus	ENSCJAG00000037305	1 retrocopy	retro_cjac_3209,
Equus caballus	ENSECAG00000024410	1 retrocopy	retro_ecab_737,
Felis catus	ENSFCAG00000024898	2 retrocopies	retro_fcat_1932, retro_fcat_2002,
Microcebus murinus	ENSMICG00000002333	2 retrocopies	retro_mmur_439, retro_mmur_707,
Mustela putorius furo	ENSMPUG00000017149	1 retrocopy	retro_mputfur_456,
Pteropus vampyrus	ENSPVAG00000012615	3 retrocopies	retro_pvam_1260, retro_pvam_1278, retro_pvam_1439,
Tursiops truncatus	ENSTTRG00000007554	2 retrocopies	retro_ttru_1311, retro_ttru_285,
Vicugna pacos	ENSVPAG00000003247	2 retrocopies	retro_vpac_308, retro_vpac_461,