RetrogeneDB ID: retro_pabe_756

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:34606111..34606671(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB8
• Ensembl ID: ENSPPYG00000002570
• Aliases: None
• Description: NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001127101]

Sequence

>retro_pabe_756
ATGGAAGTAGCCAGGGCAGGGGTCCTGGGAATCTGGTGGCTACAAAGGGCAAACCCAGAATGTGGTGTCATTGAGTGCAT
GGACATCCTTCCACATGATCAAGGACATGACCCTGGGGTTCTATTCCAAGACCCCAGAAGAATGGGCCACCGCTGCCAAG
AAGTATAATATGTGTGTGGAAGACTATCAGCCTTACTTGGATGATGGCATGGGGTAAGGTAACTACTCAAAGTTCTTTGA
CCATTCACAGTAGGAGCAGGATCTGTGGTTTGACTGGGACCACCAAGACTTAAGGTTGAACTGGGGTGAACTGATACACT
GGCATCTGGACATGTATATCAGGAACCATGTGGATATGGCCCTCCACCCCTGTTTCTTGGAATATCATGTTCAATAATCT
CTTCAGCTTCCTGACCTTCAGGAACTTTATGTTCTATGTAGTGGAGAATTATTCTACCTACCAGCCTGTGGGGTCAAAGC
AGTATCCTTTTACTAATCTGTACCTGGGACAACGCAGTAATCCCACCAAAGAACCTGAACTAGTGGTTCCCTATGAGATC

Alignment

ORF - retro_pabe_756 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVARTGVLGVQWLQRAS-WNVMPLGARTASHMTKDMFPGPYPRTPEERAAAAKKYNMRVEDYEPYPDDG
          M.VAR.GVLG..WLQRA...NV..L.A.T..HM.KDM..G.Y..TPEE.A.AAKKYNM.VEDY.PY.DDG
Retrocopy MEVARAGVLGIWWLQRAN>QNVVSLSAWTSFHMIKDMTLGFYSKTPEEWATAAKKYNMCVEDYQPYLDDG

Parental  MGYGDYPKLPDRSQHERDPWYSWDQPDLRLNWGEPMHWHLDMFNRNRVDTS-PIPVSWNVMCMQLFGFLA
          MG.G.Y.K..D.SQ.E.D.W..WD..DLRLNWGE..HWHLDM..RN.VD.....PVSWN.M...LF.FL.
Retrocopy MG*GNYSKFFDHSQ*EQDLWFDWDHQDLRLNWGELIHWHLDMYIRNHVDMA>STPVSWNIMFNNLFSFLT

Parental  FMIFMCWVGEVYPVYQPVGPKQYPYNNLYLERGGDPSKEPERVVHYEI
          F..FM..V.E.Y..YQPVG.KQYP..NLYL.....P.KEPE.VV.YEI
Retrocopy FRNFMFYVVENYSTYQPVGSKQYPFTNLYLGQRSNPTKEPELVVPYEI

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	124.68 RPM
SRP007412_cerebellum	0.00 RPM	91.08 RPM
SRP007412_heart	0.00 RPM	106.75 RPM
SRP007412_kidney	0.00 RPM	108.49 RPM
SRP007412_liver	0.00 RPM	72.37 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_756 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_756 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_756 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_770
Pan troglodytes	retro_ptro_539
Gorilla gorilla	retro_ggor_639
Macaca mulatta	retro_mmul_1098
Callithrix jacchus	retro_cjac_870

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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,