RetrogeneDB ID: retro_ptro_539

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:34695051..34695610(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB8
• Ensembl ID: ENSPTRG00000002851
• Aliases: None
• Description: Pan troglodytes NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8, 19kDa (NDUFB8), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001144864]

Sequence

>retro_ptro_539
TTGGAAGTAGCCAGGGCAGGGGTCCTGGGAATCTGGTGGCTACAAAGGGCAACCCAGAAAGTGGTGTCATTGAGTGCATG
GCCATCCTTCCACATGATCAAGGACATGCCCCTGGGGTTCTATTCCAAGACCCCAGAAGAATGGGCCACCGCTGCCAAGA
AGTATAATATGTGTGTGGAAGACTATCAGCCTTACTTGGATGATGGCATGGGGTATGGTAACTACTCAAAGTTCTTTGAC
CATTCACAGTAGGAGAGGGATCTGTGGTTTGACTGGGACCACCAAGACTTGAGGTTGAACTGGGGTGAACTGATACACTG
GCATCTGGGCATGTATATCAGGAACCATGTGGATATGGCCCTCCACCCCTGTTTCTTGGAATATCATGTTCAATAATCTC
TTCAGCTTCCTGACCTTCATGAACTTTATGTTCTATGTAGTGGAGAATTATTCTACCTACCAGCCTGTGGGGCCAAACCA
GTATCCTTTTAATAATCTGTACTTGGGACAAGGCAGTGATCCCACCAAAGAACCTGAGCTAGTGGTTCACTATGAGATC

Alignment

ORF - retro_ptro_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.1 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVARAGVLGVQWLQRASRNVMPLGARTASHMTKDMFPGPYPRTPEERAAAAKKYNMRVEDYEPYPDDGM
          ..VARAGVLG..WLQRA...V..L.A....HM.KDM..G.Y..TPEE.A.AAKKYNM.VEDY.PY.DDGM
Retrocopy LEVARAGVLGIWWLQRATQKVVSLSAWPSFHMIKDMPLGFYSKTPEEWATAAKKYNMCVEDYQPYLDDGM

Parental  GYGDYPKLPDRSQHERDPWYSWDQPGLRLNWGEPMHWHLDMYNRNRVDTS-PTPLSWHVMCMQLFGFLAF
          GYG.Y.K..D.SQ.ERD.W..WD...LRLNWGE..HWHL.MY.RN.VD....TP.SW..M...LF.FL.F
Retrocopy GYGNYSKFFDHSQ*ERDLWFDWDHQDLRLNWGELIHWHLGMYIRNHVDMA>STPVSWNIMFNNLFSFLTF

Parental  MIFMCWVGDVYPVYQPVGPKQYPYNNLYLERGGDPSKEPERVVHYEI
          M.FM..V...Y..YQPVGP.QYP.NNLYL..G.DP.KEPE.VVHYEI
Retrocopy MNFMFYVVENYSTYQPVGPNQYPFNNLYLGQGSDPTKEPELVVHYEI

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	0.00 RPM	150.18 RPM
SRP007412_cerebellum	0.00 RPM	93.74 RPM
SRP007412_heart	0.00 RPM	160.95 RPM
SRP007412_kidney	0.00 RPM	175.90 RPM
SRP007412_liver	0.00 RPM	137.81 RPM
SRP007412_testis	0.00 RPM	34.57 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_539 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_539 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_770
Gorilla gorilla	retro_ggor_639
Pongo abelii	retro_pabe_756
Macaca mulatta	retro_mmul_1098
Callithrix jacchus	retro_cjac_870

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006651	3 retrocopies	retro_amel_1460, retro_amel_1467, retro_amel_931,
Bos taurus	ENSBTAG00000000091	1 retrocopy	retro_btau_1844,
Canis familiaris	ENSCAFG00000009698	2 retrocopies	retro_cfam_1405, retro_cfam_1947,
Callithrix jacchus	ENSCJAG00000037906	1 retrocopy	retro_cjac_870,
Dasypus novemcinctus	ENSDNOG00000003661	1 retrocopy	retro_dnov_65,
Felis catus	ENSFCAG00000006453	2 retrocopies	retro_fcat_501, retro_fcat_856,
Homo sapiens	ENSG00000166136	3 retrocopies	retro_hsap_1363, retro_hsap_1772, retro_hsap_770,
Gorilla gorilla	ENSGGOG00000027239	3 retrocopies	retro_ggor_1062, retro_ggor_2240, retro_ggor_639,
Microcebus murinus	ENSMICG00000001341	1 retrocopy	retro_mmur_859,
Myotis lucifugus	ENSMLUG00000015094	1 retrocopy	retro_mluc_1830,
Macaca mulatta	ENSMMUG00000006636	5 retrocopies	retro_mmul_1098, retro_mmul_1232, retro_mmul_1620, retro_mmul_415, retro_mmul_753,
Monodelphis domestica	ENSMODG00000019356	1 retrocopy	retro_mdom_1543,
Mustela putorius furo	ENSMPUG00000016959	1 retrocopy	retro_mputfur_1259,
Mus musculus	ENSMUSG00000025204	2 retrocopies	retro_mmus_1995, retro_mmus_2909,
Nomascus leucogenys	ENSNLEG00000014774	3 retrocopies	retro_nleu_1068, retro_nleu_2810, retro_nleu_398,
Otolemur garnettii	ENSOGAG00000030711	3 retrocopies	retro_ogar_1237, retro_ogar_152, retro_ogar_2593,
Pongo abelii	ENSPPYG00000002570	3 retrocopies	retro_pabe_1131, retro_pabe_1541, retro_pabe_756,
Pan troglodytes	ENSPTRG00000002851	3 retrocopies	retro_ptro_1186, retro_ptro_539 , retro_ptro_936,
Sus scrofa	ENSSSCG00000006166	2 retrocopies	retro_sscr_1092, retro_sscr_444,
Tupaia belangeri	ENSTBEG00000000209	8 retrocopies	retro_tbel_1872, retro_tbel_2950, retro_tbel_3122, retro_tbel_322, retro_tbel_3696, retro_tbel_4042, retro_tbel_4718, retro_tbel_540,