RetrogeneDB ID: retro_ptro_1383

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:61386029..61387006(-)
• Located in intron of: ENSPTRG00000011537

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAF1
• Ensembl ID: ENSPTRG00000006945
• Aliases: None
• Description: Pan troglodytes NADH dehydrogenase (ubiquinone) complex I, assembly factor 1 (NDUFAF1), mRNA. [Source:RefSeq mRNA;Acc:NM_001079923]

Sequence

>retro_ptro_1383
ATGGCTTTGGTTCACAAATTGCTGCATGGCACTTATATTCTCAGAAAATGCTCTAAGACAACTGCTGCCTTGCATTCATT
TTTGGGTATTCACTTTGCACACCACTCCAGTAGTCTTCAGAAACCAGTGGCTTCTCCTGGCAAAGCCTCCTCACAGAGGA
ATACTGAAGGGGGTTGCCAAGGACATCACCAGAAAGAAGTTGCTTTGGATATAACTTCTCCTGAGGAGAAACCTGAAGTT
AGTTTCAATAAAGCAATTAGAGATGAAATAAAGGACAATTTTAGGCATTTGAAGGATGAAATTGTGGATCATTGGATAGG
ACCCGAAGGCCGCCCTCTGCATGAGGTCTTGCTGGAACAAGCCAAGGTTGTCTGACAGTTCTGGGGGAAAGAAGACTTGG
ATAAGTAGATAGTGACTTCTGAAAAGACGATTGGAGGCAGAAGTGAAGTATTTTTGAAAATGGGCAAGAATAACCAAAGT
GCACTGCTATATGGAACTCTGAGCTCTGAGGTGCCTCAGGATGGGGAGACTACCTGAAGTGGGTACTGTGCAATGATATC
CAGGATTCCAGGGGGTGCTTTTGAGAGGAAGATGTCTTATGATTGGTCCCAGTTCAGTACTCTGTATCTCCGTGTATGTG
GGGATGGTTGGCCTTGGATGATGAATATCAGGGAGGACACAGGTATAATCCAGAGGAAAAACAGATGTATAGTTACTTCG
TGTTCACCCGTGGGGACTCCTACTGGCAGGAGGTCAAGATCCCTTTTTCCAAATTTTTTTTCCCTAATCAAGGAAGGGTA
CAGGATGTTCAGAGTCAGCTTCTGCTTGATAAGATCTCTTCTATAGCATTCACCTTGGCTGATAAAGTGGGTGGTCCATT
CTTCCTGGAGATAGATTTTATTGGAGTGCTTACTGTTCCAGCCCACACAGAATTTGCCTATGAAAATTCTCCAGAGCTTA
ACCCAAGAATTTAAAAA

Alignment

ORF - retro_ptro_1383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALVHKLLRGTYFLRKFSKPTSALYPFLGIRFAEYSSSLQKPVASPGKASSQRKTEGDLQGDHQKEVALD
          MALVHKLL.GTY.LRK.SK.T.AL..FLGI.FA..SSSLQKPVASPGKASSQR.TEG..QG.HQKEVALD
Retrocopy MALVHKLLHGTYILRKCSKTTAALHSFLGIHFAHHSSSLQKPVASPGKASSQRNTEGGCQGHHQKEVALD

Parental  ITSSEEKPDVSFDKAIRDEAMYHFRHLKDEIVDHWRGPEGHPLHEVLLEQAKVVWQFRGKEDLDKWTVTS
          ITS.EEKP.VSF.KAIRDE....FRHLKDEIVDHW.GPEG.PLHEVLLEQAKVV.QF.GKEDLDK..VTS
Retrocopy ITSPEEKPEVSFNKAIRDEIKDNFRHLKDEIVDHWIGPEGRPLHEVLLEQAKVV*QFWGKEDLDK*IVTS

Parental  DKTIGGRSEVFLKMGKNNQSALLYGTLSSEAPQDGESTRSGYCAMISRIPRGAFERKMSYDWSQFNTLYL
          .KTIGGRSEVFLKMGKNNQSALLYGTLSSE.PQDGE.T.SGYCAMISRIP.GAFERKMSYDWSQF.TLYL
Retrocopy EKTIGGRSEVFLKMGKNNQSALLYGTLSSEVPQDGETT*SGYCAMISRIPGGAFERKMSYDWSQFSTLYL

Parental  RVRGDGRPWMVNIKEDTDFFQRTN-QMYSYFMFTRGGPYWQEVKIPFSKFFFSNRGRIRDVQHELPLDKI
          RV.GDG.PWM.NI.EDT...QR.N.QMYSYF.FTRG..YWQEVKIPFSK....N.GR..DVQ..L.LDKI
Retrocopy RVCGDGWPWMMNIREDTGIIQRKN<QMYSYFVFTRGDSYWQEVKIPFSKXXXPNQGRVQDVQSQLLLDKI

Parental  SSIGFTLADKVDGPFFLEIDFIGVFTDPAHTEEFAYENSPELNPRLFK
          SSI.FTLADKV.GPFFLEIDFIGV.T.PAHT.EFAYENSPELNPR..K
Retrocopy SSIAFTLADKVGGPFFLEIDFIGVLTVPAHT-EFAYENSPELNPRI*K

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	0.05 RPM	22.04 RPM
SRP007412_cerebellum	0.11 RPM	25.13 RPM
SRP007412_heart	0.12 RPM	61.29 RPM
SRP007412_kidney	0.16 RPM	35.75 RPM
SRP007412_liver	0.03 RPM	31.69 RPM
SRP007412_testis	0.95 RPM	123.19 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1383 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1383 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1383 has 0 orthologous retrocopies within eutheria group .

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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 ,