RetrogeneDB ID: retro_cfam_1709

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:64399161..64399863(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHBDD3
• Ensembl ID: ENSCAFG00000012114
• Aliases: None
• Description: rhomboid domain containing 3 [Source:HGNC Symbol;Acc:1308]

Sequence

>retro_cfam_1709
CTACTGTCCCCAGCGCTACCTCTTGCCTCCTCCATCCTGACGCTGCTGCTGAGCAACCTGTGGCTGGTGGGGGTGGCCCT
CGTCTTACCCTGGCCCCAGAGCTGCTGCTGGACCCTTGGCAGGCTCACTGGCTGCTGGCCCAGGCCCTGGGGTACACGGC
CAGACCTGGCCTGCTCCTGAGCCTGCTGTTCCTGCCCCCACTAGGCTGGTGGCAGCAGTGCTACCTGGGCACACTGAGGC
TCCTGCATGCCCCTGCCCTGCTCCCCCTGGCTGCTGGGCTAATAGGTGTGCTGCTGGCAGGCCTCAAGGTATCCAGTGCA
GCTGGTGGCTATGGCTACATGCCTGTCCACCAGGCCATGCTGGCAGGGCAACGTTACCACCTACACATTCCAAGGGGGTA
CTGCCACTGTGGCTGCTGCCATAGCTGCTGCTTGACTTGACACCACCGCTCAGCTCCAAGCCATCCTTCCTGCAGCTACT
CTGAAGCCTCTTGTTGGCCTGGCCTCTGCAGCCAGGGCCTTCCAGTGGTTGGAGCTCCCTGAGCTGAGGCTGCAAGCACT
GCAGGAGGGCATCTTGTGCAGGGCCCTGGCAGGATGCTGGCCACACAGACTCTGTCCTACCTCTGGTGATCTGGCCCGAG
CTACCTGTCACCCATCCTGTTGGGTGCAGCCTCTTGCCTCTGGACCTCCTTACATGGCCTCT

Alignment

ORF - retro_cfam_1709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.75 %
• Parental protein coverage: 71.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LPSPALPLASSVLMLLLSSLWLVGA-GPSLALAPELLLDPWQAHRLLTHALGHTALPGLLLSLLLLPTLG
          L.SPALPLASS.L.LLLS.LWLVG..GP.L.LAPELLLDPWQAH.LL..ALG.TA.PGLLLSLL.LP.LG
Retrocopy LLSPALPLASSILTLLLSNLWLVGV<GPRLTLAPELLLDPWQAHWLLAQALGYTARPGLLLSLLFLPPLG

Parental  WWQECHLGTLRFLHASALLALAAGLMGVLLAGLGVSSAAGGCGYMPVHLAMLAGQGYH-PRQPLGILPPW
          WWQ.C.LGTLR.LHA.ALL.LAAGL.GVLLAGL.VSSAAGG.GYMPVH.AMLAGQ.YH.P....G.LP.W
Retrocopy WWQQCYLGTLRLLHAPALLPLAAGLIGVLLAGLKVSSAAGGYGYMPVHQAMLAGQRYH<PTHSKGVLPLW

Parental  LLPWLLLALTPLLSSEPPFLQLFCGL-LAGLAYAAGAFQWLELSERRLQALQEGALCRALARCWPFRLLP
          LLP.LLL.LTP.LSS.P.FLQL...L.L.GLA.AA.AFQWLEL.E.RLQALQEG.LCRALA.CWP.RL.P
Retrocopy LLP*LLLDLTPPLSSKPSFLQLL*SL<LVGLASAARAFQWLELPELRLQALQEGILCRALAGCWPHRLCP

Parental  TPGSLA-ELPVIHPAA-ARPPTPGLPYMAS
          T.G.LA.ELPV.HP.....P...G.PYMAS
Retrocopy TSGDLA>ELPVTHPVG<VQPLASGPPYMAS

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	19.19 RPM
SRP017611_brain	0.00 RPM	13.18 RPM
SRP017611_kidney	0.00 RPM	21.53 RPM
SRP017611_liver	0.00 RPM	6.31 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1709 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1709 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012114	1 retrocopy	retro_cfam_1709 ,
Gorilla gorilla	ENSGGOG00000012202	1 retrocopy	retro_ggor_1396,