RetrogeneDB ID: retro_cfam_2182

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:73337139..73338037(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000017506
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ECHDC1
• Ensembl ID: ENSCAFG00000001069
• Aliases: None
• Description: enoyl CoA hydratase domain containing 1 [Source:HGNC Symbol;Acc:21489]

Sequence

>retro_cfam_2182
ATGGCAGGAAATCTTCTGAAGACATCATCTTTGACTGTAAGGGCAAAATTACTACATCAAACGGGGTTGTCCCTTTATAA
TACATCTCATGGCTTCCATAAGGAAGAATTTTTAAAAAAAATCAACAGTTTCCTGGTGGATCCGTTGACCTTAAGAAGGA
AGACAGTGGCATTGGTATTCTTACCCTGAACAACCCAAGTAAAATGAATGCTTTCTCAGGTTTTATGATGCTACAACTTC
TGGAAAAAATGATTGAATTGGAAAATTGGACAGAGGGGAAAGGTCTCATTGTTTGTGTGGCAAAAAATACTTTCTCCTCA
GGATCTGATCTGAATGCTGTGAAAGCACTAGCAACTCCAAAGGATGGAATGGCCTTATGTATGTTCATGCAAAACACCTT
AACAAGATTTATGAGACTCCCTTTAATAAGTGTTGCACTGATTCAAGGTCAGGCATTAGGTGGAGGAACAGAGGTTACTA
CAGCATGTGATTTCAAGCTGATGACCACAGACAGCGAGACAAGATTAGTCCACAGGAAATGGGCATAGTACCCAGCTGGG
GCAGTGCCACCCACCTGGTGGAGATCCTGGGCGCCAGGCAGGCCCTCAAGGTGCTAAGTGGAGCCGTCCACCTGAATGCG
GTGAAAGCCCTGAGCATGGGGATGGTGGAAGAGGTCCTGCGCTCCTCCGACAAGGCCGACTGTCTGCAAGAGGCACAGGC
GTGGCTAAGGCAGTTCACCAAGGGGCCTCCAGAAGTAATTAGAGCTTTGAAAAGATCGGTGTCTTCAGACAAAGAGCTCT
GTTTGGAGGAGGCTTTACAGATCAAAAAAGATCTTGTAGGAAGGGTTTGGGGTGGACCTGCAAACAAAGAGGTGATTGCT
AGGAAAGGAAAGCAAAAT

Alignment

ORF - retro_cfam_2182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.11 %
• Parental protein coverage: 99.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGNLLKTSSLSVRTKLLHQTGLSLYNTSHGFHEEDLKKKL-QQFPGGSVDLQKEDSGIGILTLNNPSKM
          MAGNLLKTSSL.VR.KLLHQTGLSLYNTSHGFH.E.......QQFPGGSVDL.KEDSGIGILTLNNPSKM
Retrocopy MAGNLLKTSSLTVRAKLLHQTGLSLYNTSHGFHKEEFXXXX<QQFPGGSVDLKKEDSGIGILTLNNPSKM

Parental  NAFSGVMMLQLLEKVIELENWTEGKGLIVRGAKNTFSSGSDLNAVKALATPEDGMALCMFMQNTLTRLMR
          NAFSG.MMLQLLEK.IELENWTEGKGLIV..AKNTFSSGSDLNAVKALATP.DGMALCMFMQNTLTR.MR
Retrocopy NAFSGFMMLQLLEKMIELENWTEGKGLIVCVAKNTFSSGSDLNAVKALATPKDGMALCMFMQNTLTRFMR

Parental  LPLISVALIQGRALGGGAEVTTACDFRLMTADGEIRFVHR-EMGIVPSWGGGTRLVELLGARQALKVLSG
          LPLISVALIQG.ALGGG.EVTTACDF.LMT.D.E.R.VHR.EMGIVPSWG..T.LVE.LGARQALKVLSG
Retrocopy LPLISVALIQGQALGGGTEVTTACDFKLMTTDSETRLVHR<EMGIVPSWGSATHLVEILGARQALKVLSG

Parental  ALPLDAARALSLGMVEEVLRASDEASCLQEARAWLGQFTQGPPQVIRALKRSVSSSRELCLEEALQMEKE
          A..L.A..ALS.GMVEEVLR.SD.A.CLQEA.AWL.QFT.GPP.VIRALKRSVSS..ELCLEEALQ..K.
Retrocopy AVHLNAVKALSMGMVEEVLRSSDKADCLQEAQAWLRQFTKGPPEVIRALKRSVSSDKELCLEEALQIKKD

Parental  LVGTVWGGPANREAIARKGKFN
          LVG.VWGGPAN.E.IARKGK.N
Retrocopy LVGRVWGGPANKEVIARKGKQN

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	36.37 RPM
SRP017611_brain	0.00 RPM	26.76 RPM
SRP017611_kidney	0.00 RPM	24.37 RPM
SRP017611_liver	0.00 RPM	29.73 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2182 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2182 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001069	1 retrocopy	retro_cfam_2182 ,
Cavia porcellus	ENSCPOG00000004786	1 retrocopy	retro_cpor_1303,
Echinops telfairi	ENSETEG00000006454	2 retrocopies	retro_etel_2049, retro_etel_564,
Mustela putorius furo	ENSMPUG00000014606	1 retrocopy	retro_mputfur_14,
Sorex araneus	ENSSARG00000011144	2 retrocopies	retro_sara_149, retro_sara_255,