RetrogeneDB ID: retro_hsap_2068

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:53727226..53727918(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000267809
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFV2
• Ensembl ID: ENSG00000178127
• Aliases: NDUFV2, CI-24k
• Description: NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa [Source:HGNC Symbol;Acc:7717]

Sequence

>retro_hsap_2068
GGAAGACATGTGAGGAATTGCATAAGACAGCTATGCAAAATGGAGCTGGAGGAGCTTTATTTGTGCACAGAGATACTCCT
GAGAATAACCCTGATACTCCATTTGATTTCACACCAGAAAACTATAAGAGGATAGAGGCAATTGTAAAAAACTATCCAGA
AGGCCATAAAGCAGCAGCTGTTCTTCCAGTCCTGGATTTAGCCCAAAGGCAGAATGGGTGGTTGCCCATCTCTGCTATGA
ACAAGGTTGCAGAAGTTTTACAAGTACCTCCAATAAGAGTATATGAAGTAGCAACTTTTTATACAATGTATAATCGAAAG
CCAGTTGAAAAGTATCACATTCAGGTCTGCACTACTACACCCTGCATGCTTCCAAACTCTGACAGCATACTGGAGGCCAT
TCAGAAAAAGCTTGGAATAAAGCTTGGGGAGACTACACCTGACAAACTTTTCACTCTTGTAGAAGTGGAATGTTTAGGGG
CCTGTGTGAACGCACCAATGGTTCAAATAAATGACAATTACTATGAAGATTTGACAGCTAAGGATATTGAAGAAATTATT
GATGAGCTCAAGGCTGGCAAAATCCCAAAACCTGGGCCAAGGAGTGGACGCTTCTCTTGTGAGCCAGCTGGAGGTCTTAC
CCCTTTGACTGAACCACCCAAGGGACCTGGATTTGGCATACAAGCAGGCCTT

Alignment

ORF - retro_hsap_2068 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.12 %
• Parental protein coverage: 91.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRHVRN-LHKTVMQNGAGGALFVHRDTPENNPDTPFDFTPENYKRIEAIVKNYPEGHKAAAVLPVLDLAQ
          GRHVRN.LHKT.MQNGAGGALFVHRDTPENNPDTPFDFTPENYKRIEAIVKNYPEGHKAAAVLPVLDLAQ
Retrocopy GRHVRN<LHKTAMQNGAGGALFVHRDTPENNPDTPFDFTPENYKRIEAIVKNYPEGHKAAAVLPVLDLAQ

Parental  RQNGWLPISAMNKVAEVLQVPPMRVYEVATFYTMYNRKPVGKYHIQVCTTTPCMLRNSDSILEAIQKKLG
          RQNGWLPISAMNKVAEVLQVPP.RVYEVATFYTMYNRKPV.KYHIQVCTTTPCML.NSDSILEAIQKKLG
Retrocopy RQNGWLPISAMNKVAEVLQVPPIRVYEVATFYTMYNRKPVEKYHIQVCTTTPCMLPNSDSILEAIQKKLG

Parental  IKVGETTPDKLFTLIEVECLGACVNAPMVQINDNYYEDLTAKDIEEIIDELKAGKIPKPGPRSGRFSCEP
          IK.GETTPDKLFTL.EVECLGACVNAPMVQINDNYYEDLTAKDIEEIIDELKAGKIPKPGPRSGRFSCEP
Retrocopy IKLGETTPDKLFTLVEVECLGACVNAPMVQINDNYYEDLTAKDIEEIIDELKAGKIPKPGPRSGRFSCEP

Parental  AGGLTSLTEPPKGPGFGVQAGL
          AGGLT.LTEPPKGPGFG.QAGL
Retrocopy AGGLTPLTEPPKGPGFGIQAGL

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
bodymap2_adipose	1.05 RPM	2.03 RPM
bodymap2_adrenal	0.37 RPM	6.08 RPM
bodymap2_brain	2.67 RPM	2.60 RPM
bodymap2_breast	0.27 RPM	2.80 RPM
bodymap2_colon	1.33 RPM	0.46 RPM
bodymap2_heart	2.57 RPM	1.03 RPM
bodymap2_kidney	0.95 RPM	0.85 RPM
bodymap2_liver	0.11 RPM	1.08 RPM
bodymap2_lung	2.07 RPM	2.39 RPM
bodymap2_lymph_node	0.82 RPM	1.44 RPM
bodymap2_ovary	0.27 RPM	1.47 RPM
bodymap2_prostate	0.55 RPM	0.74 RPM
bodymap2_skeletal_muscle	0.24 RPM	2.11 RPM
bodymap2_testis	0.79 RPM	1.68 RPM
bodymap2_thyroid	0.53 RPM	2.67 RPM
bodymap2_white_blood_cells	0.59 RPM	0.51 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2068 was not detected

EST

No EST(s) were mapped for retro_hsap_2068 retrocopy.

TSS

No TSS is located nearby retro_hsap_2068 retrocopy 5' end.

Lab

retro_hsap_2068 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2068 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007415	1 retrocopy	retro_amel_810,
Bos taurus	ENSBTAG00000004871	2 retrocopies	retro_btau_1403, retro_btau_1831,
Choloepus hoffmanni	ENSCHOG00000013714	1 retrocopy	retro_chof_1621,
Cavia porcellus	ENSCPOG00000008479	4 retrocopies	retro_cpor_1500, retro_cpor_389, retro_cpor_401, retro_cpor_689,
Dasypus novemcinctus	ENSDNOG00000017036	1 retrocopy	retro_dnov_254,
Dipodomys ordii	ENSDORG00000008179	5 retrocopies	retro_dord_161, retro_dord_233, retro_dord_327, retro_dord_503, retro_dord_750,
Erinaceus europaeus	ENSEEUG00000006818	1 retrocopy	retro_eeur_286,
Homo sapiens	ENSG00000178127	1 retrocopy	retro_hsap_2068 ,
Loxodonta africana	ENSLAFG00000010520	2 retrocopies	retro_lafr_133, retro_lafr_872,
Macaca mulatta	ENSMMUG00000022095	1 retrocopy	retro_mmul_188,
Mustela putorius furo	ENSMPUG00000004710	2 retrocopies	retro_mputfur_1106, retro_mputfur_1623,
Oryctolagus cuniculus	ENSOCUG00000009899	3 retrocopies	retro_ocun_1083, retro_ocun_1381, retro_ocun_678,
Otolemur garnettii	ENSOGAG00000010118	2 retrocopies	retro_ogar_2531, retro_ogar_3030,
Ochotona princeps	ENSOPRG00000012788	2 retrocopies	retro_opri_307, retro_opri_660,
Procavia capensis	ENSPCAG00000006284	2 retrocopies	retro_pcap_109, retro_pcap_405,
Rattus norvegicus	ENSRNOG00000042503	1 retrocopy	retro_rnor_2993,
Sorex araneus	ENSSARG00000011876	2 retrocopies	retro_sara_543, retro_sara_625,
Sus scrofa	ENSSSCG00000003683	1 retrocopy	retro_sscr_424,
Ictidomys tridecemlineatus	ENSSTOG00000016259	1 retrocopy	retro_itri_1510,
Tupaia belangeri	ENSTBEG00000015426	8 retrocopies	retro_tbel_1013, retro_tbel_1522, retro_tbel_2199, retro_tbel_2667, retro_tbel_3333, retro_tbel_3587, retro_tbel_455, retro_tbel_468,
Tursiops truncatus	ENSTTRG00000002426	3 retrocopies	retro_ttru_1543, retro_ttru_435, retro_ttru_486,