RetrogeneDB ID: retro_cfam_1500

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:19694574..19695169(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: JOSD1
• Ensembl ID: ENSCAFG00000001379
• Aliases: None
• Description: Josephin domain containing 1 [Source:HGNC Symbol;Acc:28953]

Sequence

>retro_cfam_1500
ATGAGTTCTGTGCCATGGAAGGAGACAAGGCCAAATCTGAATCTTTGGAGCTGCCCCAGGCAGCACCTCCATAAACCTAC
CATGAAAAACAGGGCAGGGAGCTTTGTGGCCTCAATAACATCTTCCAGGACAGCAAGGTCTTCATATCAGAAATGCTGCA
AGAGATTTTCCCAGGGCTATCTCCAAGCACCATGGTGAACCTCCACAAGAAGAGCATAGTAGGAAATGGGAACTATGAAG
TGAACGTCCTTTATGGCAGCACTTCAAACCATAGGCTATGCAGCAGAGTGGTGGAACAAGCCTGGGGATGTCAGTACCGC
TGCTCTCACTAACATCATGGGTTTCATCATGAATCTGGCCTCCAGCCTGTGCTGGGGTCGACTGAAGTTGCCTCTCAAAA
AGCAGCACTGGCTCTGGTTTGAGAGGCAGGAGGTGCCTACTTCAACCTCAACTCCAAACTGAAGATGCCTGAGTAGACTG
GAGGAGAAAGCCAGCTCTGGAAATTTCTAAAACATCACTTGGGAGGAGAGAACTGTGAACTCCTGCTGGTGGTGCTAGAC
AGGTGGAGGCCCATTAGAGTGGGAGCACTGATTTG

Alignment

ORF - retro_cfam_1500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSCVPWK-GDKAKSESLELPQAAPPQIYHEKQRRELCALHALNNVFQDSNAFTRETLQEIFQRLSPNTMV
          MS.VPWK.GDKAKSESLELPQAAPP..YHEKQ.RELC....LNN.FQDS..F..E.LQEIF..LSP.TMV
Retrocopy MSSVPWK<GDKAKSESLELPQAAPP*TYHEKQGRELCG---LNNIFQDSKVFISEMLQEIFPGLSPSTMV

Parental  TPHKKSMLGNGNYDVNVI-MAALQTKGYEAVWWDKRRDVSAIALTNVMGFIMNLPSSLCWGPLKLPLKRQ
          ..HKKS..GNGNY.VNV..MAALQT.GY.A.WW.K..DVS..ALTN.MGFIMNL.SSLCWG.LKLPLK.Q
Retrocopy NLHKKSIVGNGNYEVNVL>MAALQTIGYAAEWWNKPGDVSTAALTNIMGFIMNLASSLCWGRLKLPLKKQ

Parental  HWI-CVREVGGAYYNLDSKLKMPEWIGGESELRKFLKHHLRGKNCELLLVV-PEEVEARQSWRADV
          HW...V.E.GGAY.NL.SKLKMPE..GGES.L.KFLKHHL.G.NCELLLVV....VEA..S...D.
Retrocopy HWL<LV*EAGGAYFNLNSKLKMPE*TGGESQLWKFLKHHLGGENCELLLVV<ARQVEAH*SGSTDL

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	19.70 RPM
SRP017611_brain	0.00 RPM	20.01 RPM
SRP017611_kidney	0.00 RPM	9.64 RPM
SRP017611_liver	0.00 RPM	5.80 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1500 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1500 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010171	1 retrocopy	retro_btau_1508,
Canis familiaris	ENSCAFG00000001379	1 retrocopy	retro_cfam_1500 ,
Choloepus hoffmanni	ENSCHOG00000001723	2 retrocopies	retro_chof_1576, retro_chof_233,
Equus caballus	ENSECAG00000015546	1 retrocopy	retro_ecab_251,
Felis catus	ENSFCAG00000002821	1 retrocopy	retro_fcat_565,
Macropus eugenii	ENSMEUG00000002899	2 retrocopies	retro_meug_1507, retro_meug_531,
Microcebus murinus	ENSMICG00000011798	1 retrocopy	retro_mmur_1202,
Myotis lucifugus	ENSMLUG00000003764	1 retrocopy	retro_mluc_1868,
Mus musculus	ENSMUSG00000022426	1 retrocopy	retro_mmus_3014,
Otolemur garnettii	ENSOGAG00000007520	3 retrocopies	retro_ogar_1462, retro_ogar_2911, retro_ogar_3487,
Pteropus vampyrus	ENSPVAG00000010148	1 retrocopy	retro_pvam_181,
Rattus norvegicus	ENSRNOG00000014440	2 retrocopies	retro_rnor_2954, retro_rnor_906,
Sarcophilus harrisii	ENSSHAG00000015931	1 retrocopy	retro_shar_643,
Ictidomys tridecemlineatus	ENSSTOG00000024999	1 retrocopy	retro_itri_193,
Tarsius syrichta	ENSTSYG00000008846	1 retrocopy	retro_tsyr_1076,