RetrogeneDB ID: retro_ptro_1336

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:49492381..49492633(+)
• Located in intron of: ENSPTRG00000039575

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA3
• Ensembl ID: ENSPTRG00000028890
• Aliases: NDUFA3, CI-B9
• Description: Pan troglodytes NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3, 9kDa (NDUFA3), mRNA. [Source:RefSeq mRNA;Acc:NM_001251975]

Sequence

>retro_ptro_1336
ATGGCTGCAAGACTTGCTGCCTTCTTCAAGAATGCCTGGGCCAAGCAGCCAGTGCTGGCTGTGTCCTTCACCATTGCAGG
CCATGCTATAATTCTGCCCCCACTCAGCCCCTACACCAAGTATGCCATCATGATCAACCAGGCCACACCCTACAATTACC
CAATGCCTGTCTGAGATGATGGGAGCATGCCTTATGTGTCCAGCCACCCCCAGGACATCTAGGGCCCAACCCTGGAGTGG
CTGAAGAAACTG

Alignment

ORF - retro_ptro_1336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAARVGAFLKNAWDKEPVLVVSFVVGGLAVILPPLSPYFKYSVMINKATPYNYPVPVRDDGNMPDVPSHP
          MAAR..AF.KNAW.K.PVL.VSF...G.A.ILPPLSPY.KY..MIN.ATPYNYP.PV.DDG.MP.V.SHP
Retrocopy MAARLAAFFKNAWAKQPVLAVSFTIAGHAIILPPLSPYTKYAIMINQATPYNYPMPV*DDGSMPYVSSHP

Parental  QDPQGPSLEWLKKL
          QD..GP.LEWLKKL
Retrocopy QDI*GPTLEWLKKL

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
SRP007412_brain_prefrontal_cortex	0.02 RPM	64.38 RPM
SRP007412_cerebellum	0.07 RPM	15.16 RPM
SRP007412_heart	0.03 RPM	20.64 RPM
SRP007412_kidney	0.10 RPM	44.88 RPM
SRP007412_liver	0.03 RPM	21.67 RPM
SRP007412_testis	0.00 RPM	7.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1336 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1336 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1336 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 62 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007754	2 retrocopies	retro_btau_207, retro_btau_986,
Canis familiaris	ENSCAFG00000002703	4 retrocopies	retro_cfam_1103, retro_cfam_12, retro_cfam_1274, retro_cfam_695,
Callithrix jacchus	ENSCJAG00000018518	5 retrocopies	retro_cjac_188, retro_cjac_2215, retro_cjac_2526, retro_cjac_382, retro_cjac_92,
Cavia porcellus	ENSCPOG00000021937	1 retrocopy	retro_cpor_991,
Equus caballus	ENSECAG00000015897	3 retrocopies	retro_ecab_253, retro_ecab_598, retro_ecab_834,
Felis catus	ENSFCAG00000003611	6 retrocopies	retro_fcat_122, retro_fcat_1501, retro_fcat_442, retro_fcat_448, retro_fcat_839, retro_fcat_916,
Gorilla gorilla	ENSGGOG00000023650	2 retrocopies	retro_ggor_100, retro_ggor_1166,
Loxodonta africana	ENSLAFG00000018014	2 retrocopies	retro_lafr_225, retro_lafr_459,
Macropus eugenii	ENSMEUG00000002939	2 retrocopies	retro_meug_408, retro_meug_688,
Monodelphis domestica	ENSMODG00000004118	1 retrocopy	retro_mdom_404,
Mustela putorius furo	ENSMPUG00000010317	3 retrocopies	retro_mputfur_1070, retro_mputfur_124, retro_mputfur_771,
Mus musculus	ENSMUSG00000035674	3 retrocopies	retro_mmus_1843, retro_mmus_3244, retro_mmus_486,
Otolemur garnettii	ENSOGAG00000006931	10 retrocopies	retro_ogar_1056, retro_ogar_1244, retro_ogar_1260, retro_ogar_1990, retro_ogar_2128, retro_ogar_2732, retro_ogar_2970, retro_ogar_3105, retro_ogar_3427, retro_ogar_729,
Pan troglodytes	ENSPTRG00000028890	5 retrocopies	retro_ptro_1032, retro_ptro_1093, retro_ptro_1336 , retro_ptro_255, retro_ptro_842,
Pteropus vampyrus	ENSPVAG00000015560	5 retrocopies	retro_pvam_1197, retro_pvam_1261, retro_pvam_479, retro_pvam_512, retro_pvam_979,
Rattus norvegicus	ENSRNOG00000014224	1 retrocopy	retro_rnor_104,
Sarcophilus harrisii	ENSSHAG00000009016	2 retrocopies	retro_shar_167, retro_shar_207,
Sus scrofa	ENSSSCG00000003261	3 retrocopies	retro_sscr_45, retro_sscr_628, retro_sscr_97,
Ictidomys tridecemlineatus	ENSSTOG00000025377	2 retrocopies	retro_itri_1280, retro_itri_756,