RetrogeneDB ID: retro_pabe_1684

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:58327724..58328702(-)
• 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_1684
GTTCACAAATTGCTGCATGGCACTTATATTCTCAGAAAATGCTCTAAGACAACTGCTGCCTTGCATTCATGGGTATTCGC
TTTGCAGACCATTCCAGGTAGTCTTCAGAAACCAGTGGCTTCTCCTGGCCAAAGCCTCCTTCACAGAGGAAGACTGAAGG
GGGTTTGGCCAAGGGATATCACCAGAAAAGAAGTTGCCTTTTAGATATAACCTTCTCCTGAGAAGAAACCTGAAGTTAAG
TTTCAATAAAAGCAATTGGAGATGAAATAAAGGACCATTTTAGGCATTTGAAGGATCAAATTTGGATCATTGGATAGGAC
CCGAAGGCTGCCCTCTACATGAGGTCTTGCTGGAACAAGCCAAGGTTGTCTGATAGTTCTGGGGGAAAGAAGACTTGGAT
AAGTAGATAGTGACTTCTGAAAAGATGATTGGAGGCAGAAGTGAAGTATTTTTGAAAATGGGCAAGAATAACCAAAGTGC
ACTGCTATATGGAACTCTGAGCTCTGAGGTGCCTCAGGATGGGGAGACTACCTGAAGTGGGTACTGTGCAATGATATCCA
GGATTCCAGGGGGTGCTTTTGAGAGGAAGATGTCTTGTGATTGGTCCCAGTTCAGTACTCTGTATCTCCATGTACGTGGG
GATGGTTGGCCTTGGATGATGTATATCAGGGAGGACACAGATATAATCCAGAGGAAAATCAGATGTATAGTTACTTCACG
TTCACCCATGGAGAGCCCTACTGGCAGGAGGTCAAGATCCCTTTTTCCAAGTTTTTTTTCCCTAATCAAGGAAGAGCGCA
GGATGTTCAGAGTCAGCTTCCGCTTGACAAGATCTCTTCTATAGCATTCACCTTGGCTGATAAAGTGGATGGTCTTTTCT
TCCTGGAGACAGATTTTATTGGAGTGCTTACTGATCCAGCCCACATAGAAGAATTTGCCTATGAAAATTCTCCAGAGCTT
AACCCAGGACTTTTAAAA

Alignment

ORF - retro_pabe_1684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.57 %
• Parental protein coverage: 99.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  VHKLLRGTYILRKFSKPASALYPFLGIRFAEYSSSLQKPVASPG-KAS-SQRKTEGDL-QGDHQK-EVAL
          VHKLL.GTYILRK.SK...AL.............SLQKPVASPG.KAS.SQRKTEG.L..G.HQK....L
Retrocopy VHKLLHGTYILRKCSKTTAALHSWV-FALQTIPGSLQKPVASPG>KAS>SQRKTEGGLAKGYHQKRSCLL

Parental  DIT-SSEEKPDV-SFDK-AIRDEAAYHFRHLKDEI-VDHWRGPEGRPLREVLLEQAKVVWQFRGKEDLDK
          DIT.S.E.KP.V.SF.K.AI.DE...HFRHLKD.I..DHW.GPEG.PL.EVLLEQAKVV..F.GKEDLDK
Retrocopy DIT>SPEKKPEV>SFNK>AIGDEIKDHFRHLKDQI<LDHWIGPEGCPLHEVLLEQAKVV**FWGKEDLDK

Parental  WTVTSDKTIGGRSEVFLKMGKNNQSALLYGTLSSEAPHDGESTRSGYCAMISRIPRGAFERKVSYDWSQF
          ..VTS.K.IGGRSEVFLKMGKNNQSALLYGTLSSE.P.DGE.T.SGYCAMISRIP.GAFERK.S.DWSQF
Retrocopy *IVTSEKMIGGRSEVFLKMGKNNQSALLYGTLSSEVPQDGETT*SGYCAMISRIPGGAFERKMSCDWSQF

Parental  NTLYLRVRGDGRPWMVNIKEDTDFFQR-TNQMYSYFMFTRGGPYWQEVKIPFSKFFFSNRGRIRDVQHEL
          .TLYL.VRGDG.PWM..I.EDTD..QR..NQMYSYF.FT.G.PYWQEVKIPFSK....N.GR..DVQ..L
Retrocopy STLYLHVRGDGWPWMMYIREDTDIIQR<ENQMYSYFTFTHGEPYWQEVKIPFSKXXXPNQGRAQDVQSQL

Parental  PLDKISSIGFTLADKVDGPFFLEIDFIGVFTDPAHTEEFAYENSPELNPRLFK
          PLDKISSI.FTLADKVDG.FFLE.DFIGV.TDPAH.EEFAYENSPELNP.L.K
Retrocopy PLDKISSIAFTLADKVDGLFFLETDFIGVLTDPAHIEEFAYENSPELNPGLLK

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	0.17 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_1684 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1684 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1684 has 0 orthologous retrocopies within eutheria group .

---

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,