RetrogeneDB ID: retro_ocun_936

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:29233910..29234281(-)
• Located in intron of: ENSOCUG00000012331

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC15
• Ensembl ID: ENSOCUG00000001696
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 15 [Source:HGNC Symbol;Acc:20325]

Sequence

>retro_ocun_936
GGCAATGGACCATGTGGCACTAAGTATCTGCTGCCCTCAGCCCAACAGTTGGACACTGAGAGCCACCAGGCTCTGGCAAG
AAGTCTGACAGCTGTAGGACTGGGTATTAAAGGCTCTTGCACTTGCAGGTCAGTTAAGGATTTCATATCTGGAATAAGTA
ATCACAGGAACTGCAAGGAAGATTTCAACTCCGAACCTTTCATTCTACTATGAAGGAGGATTTAAACAGAAAACGAGTGG
GTGAGAAGTTAAGTTTTATTTTAGGTGGAAGCCCATCTGCTAGCAAGGCCTAAATTAGAACATTTCACTGGAGAATCATG
ATTTTGAATCACTGAGATAAAGGTAGATTTCCTTACTTAACAACCAAAATA

Alignment

ORF - retro_ocun_936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.81 %
• Parental protein coverage: 84.56 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GEGLRYAEYVPPSAKRPDAEIDHGLARSLIAVGLGVA-ALAFAGRYAFQIWKPLEQVITEATRKISTPSF
          G.G.....Y..PSA...D.E....LARSL.AVGLG...ALA.AG.........LE.VIT...RKISTP..
Retrocopy GNGPCGTKYLLPSAQQLDTESHQALARSLTAVGLGIK>ALALAGQLRISY---LE*VITGTARKISTPNL

Parental  SSYYKGGFEQKMSRREA-SLILGVSPSAGKAKIRTAHRRIMILNHPDKGGSPYLATKI
          S.YY.GGF.QK.S..E..S.ILG.SPSA.KA.IRT.H.RIMILNH.DKG..PYL.TKI
Retrocopy SFYYEGGFKQKTSG*EV>SFILGGSPSASKA*IRTFHWRIMILNH*DKGRFPYLTTKI

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
SRP017611_brain	0.00 RPM	11.98 RPM
SRP017611_kidney	0.00 RPM	17.94 RPM
SRP017611_liver	0.00 RPM	2.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_936 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_936 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_936 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034785	1 retrocopy	retro_btau_1624,
Canis familiaris	ENSCAFG00000004664	1 retrocopy	retro_cfam_939,
Callithrix jacchus	ENSCJAG00000017589	2 retrocopies	retro_cjac_1663, retro_cjac_634,
Cavia porcellus	ENSCPOG00000003485	1 retrocopy	retro_cpor_327,
Equus caballus	ENSECAG00000007757	1 retrocopy	retro_ecab_561,
Erinaceus europaeus	ENSEEUG00000008785	5 retrocopies	retro_eeur_360, retro_eeur_608, retro_eeur_64, retro_eeur_93, retro_eeur_95,
Felis catus	ENSFCAG00000022632	1 retrocopy	retro_fcat_259,
Homo sapiens	ENSG00000120675	2 retrocopies	retro_hsap_3331, retro_hsap_4312,
Gorilla gorilla	ENSGGOG00000016338	2 retrocopies	retro_ggor_1294, retro_ggor_2882,
Loxodonta africana	ENSLAFG00000004343	2 retrocopies	retro_lafr_287, retro_lafr_942,
Myotis lucifugus	ENSMLUG00000008684	3 retrocopies	retro_mluc_1358, retro_mluc_1544, retro_mluc_520,
Macaca mulatta	ENSMMUG00000013689	1 retrocopy	retro_mmul_1169,
Mustela putorius furo	ENSMPUG00000001704	1 retrocopy	retro_mputfur_1065,
Nomascus leucogenys	ENSNLEG00000001759	4 retrocopies	retro_nleu_1408, retro_nleu_1464, retro_nleu_1675, retro_nleu_585,
Oryctolagus cuniculus	ENSOCUG00000001696	4 retrocopies	retro_ocun_1101, retro_ocun_487, retro_ocun_882, retro_ocun_936 ,
Oryctolagus cuniculus	ENSOCUG00000014043	5 retrocopies	retro_ocun_1100, retro_ocun_1650, retro_ocun_1869, retro_ocun_334, retro_ocun_398,
Ochotona princeps	ENSOPRG00000016191	5 retrocopies	retro_opri_1038, retro_opri_235, retro_opri_285, retro_opri_756, retro_opri_766,
Pongo abelii	ENSPPYG00000005323	1 retrocopy	retro_pabe_3508,
Pan troglodytes	ENSPTRG00000005831	2 retrocopies	retro_ptro_2148, retro_ptro_2920,
Pteropus vampyrus	ENSPVAG00000011281	1 retrocopy	retro_pvam_807,
Sorex araneus	ENSSARG00000007683	1 retrocopy	retro_sara_658,
Ictidomys tridecemlineatus	ENSSTOG00000012805	1 retrocopy	retro_itri_1710,
Taeniopygia guttata	ENSTGUG00000012364	2 retrocopies	retro_tgut_20, retro_tgut_45,
Tursiops truncatus	ENSTTRG00000015580	1 retrocopy	retro_ttru_1021,
Vicugna pacos	ENSVPAG00000001445	1 retrocopy	retro_vpac_113,