RetrogeneDB ID: retro_ptro_1691

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:131769754..131771062(-)
• Located in intron of: ENSPTRG00000012461

Retrocopy information

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

Parental gene information

• Parental gene symbol: NEK2
• Ensembl ID: ENSPTRG00000001953
• Aliases: None
• Description: None

Sequence

>retro_ptro_1691
ATGCCGTCCCAGGCTGAGAACTATGAAGTGTTGTACGCCATTGGCACAGGCTCCTATGGCCGCTGCCAGAAGATCCAGAG
GAAGAGTGACAGCAAGATACTAGTTTGGAAAGAACTTCATTATGGCTCCATGACAGAAGCTGAGAAACAGATGCTTGTTT
CTGAAGTGAATTTGCTTTGTGAACTGAAAAATCCAAACATCGTTCATTACTATGATCTTATTATTGACCGGACCAACACA
ACACTGTATATTGTAATGGAATATTGTGAAGAAGGAGACCTGGCTAGTGTAATTACAAAGGGAACCAAGGAAAGGCAATA
CTTATATGAAGAGTTTGTTCTTCGAGTGACGACTCAGTTGACTCTGGCCCTGAAGTAATGCCACACACGAAGTGATGGTG
ATCATACTGTAGTGCGTCGGGATCTGAAACCAGCCAGTGTTTTCCTGGATGGCAAGCAAAACGTCAAGCTTGGAGATTTG
GGGCTAGCCAGAATATTAAACCACGACACGAGTTTTGTAAAAACATTTGTTGGCACACCTTATTACATGTCTCCTGAACA
AACAATCACATGTCCTACAATGAAAAACAAGATATCTGGTCTTTGGGCTGTTTTGCTGTATGAATAAGGTGCATTAATGC
CTCCATTTACAGCTTTTAGCCAGAAAGACTCGCTGGGAAAATCAGAGAAGGCAAATTCAGGCAAATTCTATACCGTGACT
CTGACGAATTGAATGAAATTATTATGAGGATGTTAAAGGATTACCATCGACCTTCTGTTGAAGAAATTCTCGAGAACCCT
TTAATAGCAGATTTGGTTGCAGAAGAACAAAGAAGAAATCTTGAGAGAAGAGGGCGACAATTAGGAGAGCCAGAAAAATT
GCAGGATTCCAGCCCTGTATTGAGTGAGCTGAAACTAAAGGAAATTCAGTTAGAGGAGCGAGAGCGAGCTCTCAAAGCAA
GAGAAGAAAGATTGGAGCAGAAAGAACAAGAGTTTTGTGTCCGTGAGAGACTAGCAGAGGACAGACTGGCTAGAGCAGAA
AATGTGTTGAAGAATTACAGCTTGCTAAAGAAGTTCCTGTCTCTGGCAAGTAGTCCAGAACTTCTTAATCTTCCATCCTC
AGTAATTAAGAAGAAAGGTCATTTCAGTGGGGAAAGTAAAGAGAATGTCATGAGGAGTGAGAATTCTAAGAGTCAGCTCA
CATCTAAGTCCAAGTGCAAGGACCTTCAGGTCCTTGCTTCATGCTTCATGCTGCCCAGCTGCGGGCTCAAGCCCTGTCAG
ATATTGAGAAAAATTATCAACTAAAAAG

Alignment

ORF - retro_ptro_1691 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.01 %
• Parental protein coverage: 98.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPSRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRY
          MPS.AE.YEVLY.IGTGSYGRCQKI.RKSD.KILVWKEL.YGSMTEAEKQMLVSEVNLL.ELK.PNIV.Y
Retrocopy MPSQAENYEVLYAIGTGSYGRCQKIQRKSDSKILVWKELHYGSMTEAEKQMLVSEVNLLCELKNPNIVHY

Parental  YDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHR
          YD.IIDRTNTTLYIVMEYCE.GDLASVITKGTKERQYL.EEFVLRV.TQLTLALK.CH.RSDG.HTV..R
Retrocopy YDLIIDRTNTTLYIVMEYCEEGDLASVITKGTKERQYLYEEFVLRVTTQLTLALK*CHTRSDGDHTVVRR

Parental  DLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKTFVGTPYYMSPEQM-NRMSYNEKSDIWSLGC-LLYE
          DLKPA.VFLDGKQNVKLGD.GLARILNHDTSF.KTFVGTPYYMSPEQ..N.MSYNEK.DIWSLGC.LLYE
Retrocopy DLKPASVFLDGKQNVKLGDLGLARILNHDTSFVKTFVGTPYYMSPEQT<NHMSYNEKQDIWSLGC>LLYE

Parental  LCALMPPFTAFSQKE-LAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLIADLVAD
          ..ALMPPFTAFSQK..LAGKIREGKFR.I.YR.SDELNEII.RM..LKDYHRPSVEEILENPLIADLVA.
Retrocopy *GALMPPFTAFSQKD<LAGKIREGKFRQILYRDSDELNEIIMRM--LKDYHRPSVEEILENPLIADLVAE

Parental  EQRRNLERRGRQLGEPEKSQDSSPVLSELKLKEIQLQERERALKAREESLEQKEQELCVRERLAEDKLAR
          EQRRNLERRGRQLGEPEK.QDSSPVLSELKLKEIQL.ERERALKAREE.LEQKEQE.CVRERLAED.LAR
Retrocopy EQRRNLERRGRQLGEPEKLQDSSPVLSELKLKEIQLEERERALKAREERLEQKEQEFCVRERLAEDRLAR

Parental  AENLLKNYSLLKERKFLSLASNPELLNLPSSVIKKKVHFSGESKENIMRSENSESQLTSKSKCKDL-KKR
          AEN.LKNYSLLK..KFLSLAS.PELLNLPSSVIKKK.HFSGESKEN.MRSENS.SQLTSKSKCKDL....
Retrocopy AENVLKNYSLLK--KFLSLASSPELLNLPSSVIKKKGHFSGESKENVMRSENSKSQLTSKSKCKDL>RSL

Parental  LHAAQLRAQALSDIEKNYQLKSRQ
          LHA....A...S.......L....
Retrocopy LHASCCPAAGSSPVRY*EKLSTKK

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	1.22 RPM
SRP007412_cerebellum	0.00 RPM	0.57 RPM
SRP007412_heart	0.00 RPM	0.41 RPM
SRP007412_kidney	0.00 RPM	0.34 RPM
SRP007412_liver	0.00 RPM	1.80 RPM
SRP007412_testis	0.11 RPM	239.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1691 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1691 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1691 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2317

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000117650	4 retrocopies	retro_hsap_1301, retro_hsap_1385, retro_hsap_2317, retro_hsap_2538,
Gorilla gorilla	ENSGGOG00000005439	1 retrocopy	retro_ggor_1018,
Myotis lucifugus	ENSMLUG00000011281	1 retrocopy	retro_mluc_22,
Pan troglodytes	ENSPTRG00000001953	2 retrocopies	retro_ptro_1691 , retro_ptro_890,
Rattus norvegicus	ENSRNOG00000004487	1 retrocopy	retro_rnor_2552,