RetrogeneDB ID: retro_pabe_1960

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:68995786..68996631(+)
• Located in intron of: ENSPPYG00000012462

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC1P5
• Ensembl ID: ENSPPYG00000018554
• Aliases: VDAC1P5, VDAC3, VDAC5P
• Description: voltage-dependent anion-selective channel protein 3 [Source:RefSeq peptide;Acc:NP_001127515]

Sequence

>retro_pabe_1960
ATGGTTATGCCTCCCACGTACGCTGATCTTGGCAAATCTGCCAGGGATGTGTTCACCAAGGGCTATGGATTTGGCTTAAT
AAAACTTGATTTGAAAACAAAATCTGAGAAGGGATTGGAATTTGCAAACTTAGGCTCAGCCAACACTGAGGCCACCAAAG
TGACTGGCAGTCTGAGAACCAAGTACAGATGGACCAGATATGGCCTGACGATTATGGAGAAATGAAACACTGACCACACA
GCGGGCATGGATTGTGTGGAGGACCAGCTTGCATGTGGACTGAAGCTAACCTTTGATTCATCGCTTCTCACCTAACGCTG
GGGGAAAAAAATGCTAAATCAAAACTGCTATAGGCAGGAGCATATCAACCTGGGTTGCACCGTGGATTTTGACATTGTTG
AGCCTTCAATCTGGGGTGCTCTAGTGCTGGGTTATGAGGGCTGGCTGGCTGGCTACCGGATGAATTTTGAGACCACAGAG
TTTTAAGAGACCCAGAGGGACTTTACTCTTGGCTACGAGACTGATGAATTCCAGCTTCACACTTACGTGAATGATGGGGC
AGAGTTTGGCACCTCTGTTTCCCAGAGGTGAATAAGAAGTTGCAGACTGCTGTTAAGCTTGCCTGGACATCAGGAAACGG
TAACACACACTTCAGAACAGCAGGCAAGTGTCAGATGGACCCTGATGCCTGCTTCTTGGCTAAAGTGTACAACCCTAGCC
TGATAGGTTTAGGGTACACTCAGACCGTAAAGCCAAGTATCAAGCTGATGCTGTCAGCTCAGCTGGATGGCAAGAACGTC
GATGCTGGTGGCCATGAGTTTGGTCTAGGACTAGAATTTCAAGCA

Alignment

ORF - retro_pabe_1960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.1 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MCNTPTYCDLGKAAKDVFNKGYGFGMVKIDLKTKSCSGVEFSTSGHAYTDTGKASGNLETKYKVCNYGLT
          M...PTY.DLGK.A.DVF.KGYGFG..K.DLKTKS..G.EF...G.A.T...K..G.L.TKY....YGLT
Retrocopy MVMPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSEKGLEFANLGSANTEATKVTGSLRTKYRWTRYGLT

Parental  FTQKWNTDNTLGTEISWENKLAEGLKLTLDTI-FVPNTGKKSGKLKAS-YKRDCFSVGSNVDIDFSGPTI
          ...K.NTD.T.G.....E..LA.GLKLT.D...F.PN.G.K....K...Y.......G..VD.D...P.I
Retrocopy IMEK*NTDHTAGMDCV-EDQLACGLKLTFDSS>FSPNAGGKKC*IKTA<YRQEHINLGCTVDFDIVEPSI

Parental  YGWAVLAFEGWLAGYQMSFDTAKSKLSQNNFALGYKAADFQLHTHVNDGTEFGGSIYQK-VNEKIETSIN
          .G..VL..EGWLAGY.M.F.T......Q..F.LGY....FQLHT.VNDG.EFG.S..Q..VN.K..T...
Retrocopy WGALVLGYEGWLAGYRMNFETTEF*ETQRDFTLGYETDEFQLHTYVNDGAEFGTSVSQR<VNKKLQTAVK

Parental  LAWTAGSNNTRFGIAAKYMLDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTLSALIDGKNFSAGGHKVGL
          LAWT.G..NT.F..A.K...D......AKV.N.SLIGLGYTQT..P..KL.LSA..DGKN..AGGH..GL
Retrocopy LAWTSGNGNTHFRTAGKCQMDPDACFLAKVYNPSLIGLGYTQTVKPSIKLMLSAQLDGKNVDAGGHEFGL

Parental  GFELEA
          G.E..A
Retrocopy GLEFQA

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	0.11 RPM	93.83 RPM
SRP007412_cerebellum	0.00 RPM	124.15 RPM
SRP007412_heart	0.00 RPM	133.06 RPM
SRP007412_kidney	0.00 RPM	35.57 RPM
SRP007412_liver	0.00 RPM	38.44 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1960 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1960 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2250
Gorilla gorilla	retro_ggor_1677

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005095	1 retrocopy	retro_amel_729,
Bos taurus	ENSBTAG00000014068	4 retrocopies	retro_btau_1537, retro_btau_1607, retro_btau_365, retro_btau_685,
Canis familiaris	ENSCAFG00000005502	5 retrocopies	retro_cfam_1513, retro_cfam_2146, retro_cfam_258, retro_cfam_665, retro_cfam_713,
Choloepus hoffmanni	ENSCHOG00000007369	1 retrocopy	retro_chof_16,
Dasypus novemcinctus	ENSDNOG00000013885	1 retrocopy	retro_dnov_1753,
Equus caballus	ENSECAG00000000438	1 retrocopy	retro_ecab_799,
Felis catus	ENSFCAG00000010075	2 retrocopies	retro_fcat_1985, retro_fcat_599,
Homo sapiens	ENSG00000078668	1 retrocopy	retro_hsap_1375,
Gallus gallus	ENSGALG00000003755	1 retrocopy	retro_ggal_11,
Gorilla gorilla	ENSGGOG00000001932	2 retrocopies	retro_ggor_1071, retro_ggor_3043,
Microcebus murinus	ENSMICG00000010235	1 retrocopy	retro_mmur_1361,
Monodelphis domestica	ENSMODG00000015526	5 retrocopies	retro_mdom_1130, retro_mdom_1331, retro_mdom_1869, retro_mdom_420, retro_mdom_669,
Mus musculus	ENSMUSG00000008892	2 retrocopies	retro_mmus_110, retro_mmus_1505,
Nomascus leucogenys	ENSNLEG00000012890	1 retrocopy	retro_nleu_2593,
Otolemur garnettii	ENSOGAG00000016163	4 retrocopies	retro_ogar_2770, retro_ogar_2870, retro_ogar_589, retro_ogar_995,
Pongo abelii	ENSPPYG00000015781	6 retrocopies	retro_pabe_1042, retro_pabe_1733, retro_pabe_273, retro_pabe_2913, retro_pabe_3756, retro_pabe_700,
Pongo abelii	ENSPPYG00000018554	8 retrocopies	retro_pabe_1145, retro_pabe_1960 , retro_pabe_2304, retro_pabe_3163, retro_pabe_3665, retro_pabe_3791, retro_pabe_819, retro_pabe_971,
Pan troglodytes	ENSPTRG00000020205	2 retrocopies	retro_ptro_2548, retro_ptro_945,
Pteropus vampyrus	ENSPVAG00000014822	2 retrocopies	retro_pvam_637, retro_pvam_907,
Rattus norvegicus	ENSRNOG00000019277	1 retrocopy	retro_rnor_1596,
Sarcophilus harrisii	ENSSHAG00000017953	1 retrocopy	retro_shar_658,
Tupaia belangeri	ENSTBEG00000007420	4 retrocopies	retro_tbel_1801, retro_tbel_2150, retro_tbel_2261, retro_tbel_884,
Tarsius syrichta	ENSTSYG00000007112	1 retrocopy	retro_tsyr_918,