RetrogeneDB ID: retro_pabe_1683

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:58311212..58311962(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAF1
• Ensembl ID: ENSPPYG00000006373
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) complex I, assembly factor 1 [Source:HGNC Symbol;Acc:18828]

Sequence

>retro_pabe_1683
TTCATGGGTATTCGCTTTGCAGACCATTCCAGTAGTCTTCAGAAACCAGTGGCTTCTCCTGGCAAAGCCTCCTCACAGAG
GAAGACTGAAGGGGGTTGGCAAGGATATCACCAGAAAGAAGTTGCTTTGGATATAACTTCTCCAGAGAAGAAACCTGAAG
TTCGTTTCAATAAAGCAATTGGAGATGAAATAAAGGACCATTTTAGGCATTTGAAGGATCAAATTTGGATCATTGGATAG
GACCCGAAGGCCGCCCTCTACATGAGGTCTTGCTGGAACAAGCCAAGGTTGTCTGATAGTTCTGGGGGAAAGAAGACTTG
GATAAGTAGATAGTGACTTCTGAAAAGATGATTGGAGGCAGAAGTGAAGTATTTTTGAAAATGGGCAAGAATAACCAAAG
TGCACGCTATATGGAACTCTGAGCTCTGAGGTGCCTCAGGATGGGGAGACTACCTGAAGTGGGTACTGTGCAATGATATC
CAGGATTCCAGGGGGTGCTTTTGAGAGGAAGATGTCTTGTGATTGGTCCCAGTTCAGTACTCTGTATCTCCATGTACGTG
GGGATGGTTGGCCTTGGATGATGTATATCAGGGAGGACACAGATATAATCCAGAGGAAAATCAGATGTATAGTTACTTCA
CGTTCACCCATGGGGAGCCCTACTGGCAGAAGGTCAAGATCCCTTTTTCCAAGTTTTTTTTCCCTAATCAAGGAAGAGCG
CAGGATGTTCAGAGTCAGCTTCCGCTTGAC

Alignment

ORF - retro_pabe_1683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.77 %
• Parental protein coverage: 76.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FLGIRFAEYSSSLQKPVASPGKASSQRKTEGDLQGDHQKEVALDITSSEEKPDVSFDKAIRDEAAYHFRH
          F.GIRFA..SSSLQKPVASPGKASSQRKTEG..QG.HQKEVALDITS.E.KP.V.F.KAI.DE...HFRH
Retrocopy FMGIRFADHSSSLQKPVASPGKASSQRKTEGGWQGYHQKEVALDITSPEKKPEVRFNKAIGDEIKDHFRH

Parental  LKDEI-VDHWRGPEGRPLREVLLEQAKVVWQFRGKEDLDKWTVTSDKTIGGRSEVFLKMGKNNQSA-LLY
          LKD.I..DHW.GPEGRPL.EVLLEQAKVV..F.GKEDLDK..VTS.K.IGGRSEVFLKMGKNNQSA..LY
Retrocopy LKDQI<LDHWIGPEGRPLHEVLLEQAKVV**FWGKEDLDK*IVTSEKMIGGRSEVFLKMGKNNQSA<TLY

Parental  GTLSSEAPHDGESTRSGYCAMISRIPRGAFERKVSYDWSQFNTLYLRVRGDGRPWMVNIKEDTDFFQR-T
          GTLSSE.P.DGE.T.SGYCAMISRIP.GAFERK.S.DWSQF.TLYL.VRGDG.PWM..I.EDTD..QR..
Retrocopy GTLSSEVPQDGETT*SGYCAMISRIPGGAFERKMSCDWSQFSTLYLHVRGDGWPWMMYIREDTDIIQR<E

Parental  NQMYSYFMFTRGGPYWQEVKIPFSKFFFSNRGRIRDVQHELPLD
          NQMYSYF.FT.G.PYWQ.VKIPFSK....N.GR..DVQ..LPLD
Retrocopy NQMYSYFTFTHGEPYWQKVKIPFSKXXXPNQGRAQDVQSQLPLD

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	0.06 RPM	19.52 RPM
SRP007412_cerebellum	0.12 RPM	10.09 RPM
SRP007412_heart	0.00 RPM	22.88 RPM
SRP007412_kidney	0.00 RPM	34.17 RPM
SRP007412_liver	0.00 RPM	21.64 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1683 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1683 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1683 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1492

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000025980	1 retrocopy	retro_ggor_1492,
Microcebus murinus	ENSMICG00000016845	1 retrocopy	retro_mmur_637,
Nomascus leucogenys	ENSNLEG00000003587	1 retrocopy	retro_nleu_2733,
Pongo abelii	ENSPPYG00000006373	2 retrocopies	retro_pabe_1683 , retro_pabe_1684,
Pan troglodytes	ENSPTRG00000006945	1 retrocopy	retro_ptro_1383,