RetrogeneDB ID: retro_cfam_2081

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:51649138..51649587(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DTWD1
• Ensembl ID: ENSCAFG00000014926
• Aliases: None
• Description: DTW domain containing 1 [Source:HGNC Symbol;Acc:30926]

Sequence

>retro_cfam_2081
ATGTCTCTCAATCCATCTATATTTCCCAAAGAAAAAGAAAAAAATAATTCAAAATTTGTGGAAACACAACACTCACAAAC
TACCCCATAGCTGCAGAAGATCCTCTTCAAAACTTATGCTTAGCATCTCAAGAAGTTCTTCAATAAGTTCAGCAAAGTGA
AAGATCAAAATGTCTCAAGTGTGGTGGTTCAGGAATGTTCTATTGCCATACATATTATGTCCCAGTTGAAAATGTACCTA
TTGAACAGATGCCAGTTGTGAAGCTTCCACTGAAGATTAATATCATTAAACATTCAAATTAAACAGATGGCAAAAGTACT
GCTATACATGCAAAACTATTAGCACCTGAATTTTTAAATATTTACATATATCCTTTTATTCCAGAATATTAAGAAAAGGC
CCATGAAGTTGCACTTGTGTTTCCTGGACCTAAGTCTGTCTCAATAAGA

Alignment

ORF - retro_cfam_2081 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.13 %
• Parental protein coverage: 50.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLNPPIFLKEKEENNSKFVEIQHSQTTS-IAAEDPLQNLRLASQEVLQKAQQSGRSKCLKCGGSRMFYC
          MSLNP.IF.......NSKFVE.QHSQTT..IAAEDPLQNL.LASQEVLQ..QQS.RSKCLKCGGS.MFYC
Retrocopy MSLNPSIFPXXXXXXNSKFVETQHSQTTP<IAAEDPLQNLCLASQEVLQ*VQQSERSKCLKCGGSGMFYC

Parental  YTCYVPVENVPIEQMPLVKLPLKIDIIKHPNETDGKSTAIHAKLLAPDFVNIYTYPCIPEYEEKDHEVAL
          .T.YVPVENVPIEQMP.VKLPLKI.IIKH.N.TDGKSTAIHAKLLAP.F.NIY.YP.IPEY.EK.HEVAL
Retrocopy HTYYVPVENVPIEQMPVVKLPLKINIIKHSN*TDGKSTAIHAKLLAPEFLNIYIYPFIPEY*EKAHEVAL

Parental  VFPGPNSVSIK
          VFPGP.SVSI.
Retrocopy VFPGPKSVSIR

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	8.69 RPM
SRP017611_brain	0.00 RPM	5.16 RPM
SRP017611_kidney	0.00 RPM	17.50 RPM
SRP017611_liver	0.00 RPM	4.79 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2081 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2081 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2081 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014926	1 retrocopy	retro_cfam_2081 ,
Cavia porcellus	ENSCPOG00000003461	2 retrocopies	retro_cpor_1476, retro_cpor_250,
Homo sapiens	ENSG00000104047	1 retrocopy	retro_hsap_2846,
Gorilla gorilla	ENSGGOG00000027921	1 retrocopy	retro_ggor_1973,
Nomascus leucogenys	ENSNLEG00000006167	1 retrocopy	retro_nleu_1598,
Otolemur garnettii	ENSOGAG00000013291	1 retrocopy	retro_ogar_499,
Ochotona princeps	ENSOPRG00000002951	2 retrocopies	retro_opri_136, retro_opri_949,
Pongo abelii	ENSPPYG00000006464	2 retrocopies	retro_pabe_2355, retro_pabe_2356,
Pan troglodytes	ENSPTRG00000007058	1 retrocopy	retro_ptro_1928,
Vicugna pacos	ENSVPAG00000008358	2 retrocopies	retro_vpac_509, retro_vpac_530,