RetrogeneDB ID: retro_ptro_3182

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:8863799..8865036(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOLC1
• Ensembl ID: ENSPTRG00000023882
• Aliases: None
• Description: Nucleolar and coiled-body phosphoprotein 1 [Source:UniProtKB/TrEMBL;Acc:K7BUI5]

Sequence

>retro_ptro_3182
CCAGATCCCTAAAGTTCAGTGCCCCCGTCCTGCTCCCCCATCAAAGAAGTCCTTGGGAACCCAGGCTCCCAAGAAAGCTG
TGGAGAAGAAACAGCCTTCCGAAAGCAGTGAAGACAGCAGCGACGAGTCTGATTCAAGTTTGGAGGAAGAGGATGAACTC
TTGCTAAGTCAGTCATCTCTAAAGCAAATACTAAACAACCTCCAGCCAAGAAAGCAGCAGAGAGCTCTTCAGACAGCTCA
TATTCCAACAGTTCTGAGGATGATGAAGCTCTTTCCAAGCTAGCCAGTACCAGCAAGAATTCCTCAAATAAGCCAGCTGC
CACTACCAAGTCACCTGCAACGGAGCCAGCTGCAACTCTCAAGCAACCTGCAAGCAGTGGCCAGAAGCCTCTGATGAGAA
AGGCTGACAGCAACTCCAGTGAGAAAGAGAGCAGTTCCAGTGAGGAGGAGAAGACAAAGATGACTGTGGACCCCCTTAAG
CCCAAGGTAACTGACAAAGCAGCTCCATATCTGCCTGCCAAGCAGGCTCCTGAGAGGAGTAAGGACAGCAGCTCTCATTC
AGACAGCTCCAGCAGTGAGGAGGAGGAGGAGGAAGAGAAGACATCTAAATCCCCAGTTAAGAAGAAGTTGCAGAAGGCAG
CAGGAGGGACAGCCCCTTCCAAGCCAGCCTCCACAAAGAAAGGAAAGGTCAAGAGCAGCAGCAATTCTTCCTCTGATGAC
TCCAGTGAGGAAGAGGAAGCGAAGCCCAAGGGCAAGGACTCTCCAAGACCACAAGTCCCCAAGGCCAATGGCACCTCTGC
ACTGACTGCCCAGAATGGAAAAGCAGCTAAGAACAGCGAGGAGGAGGAAGAGGAGGAAGACAAAAAGAAAAAGGCAGCAG
TGGTAGTTTCCAAGCTGGGTTCAGGAAAGAAGTGGAAGCAGCTGAGACTGCCAAAGAGGCAGAGACTCCTCCAGCCAAGA
AAATAAAGCTTCAGACCCCTAACACATTTCCAAAAAGGAAGAAAGAAGAAAAAAGGGCATGATCCACATTCTTAAGGGTC
AGGGAGGAGGAAATTCAGGCGGCAGACAACTCCATTGATGCCAACTGAGGTGCAGCCGGAGACTGGGGGAACGAGCCAAT
GAGGTTTTGAGGTTCACCAAAGGCAAATCCTTCTGGTATGAGAAAACCAAGAAGCAGGGCATCTCCTGGGAAGGCTCAAT
CTCTGTCCAGGTCAATTCTATTAATTTTGAAAGTGAG

Alignment

ORF - retro_ptro_3182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.18 %
• Parental protein coverage: 58.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PGPYSSVPPPS-APLPKKSLGTQPPKKAVEKQQPVESSEDSSDECDSSSEEEKK-PPTKAVVSKATTKPP
          P.P.SSVP.PS.AP..KKSLGTQ.PKKAVEK.QP.ESSEDSSDE.DSS.EEE......K.V.SKA.TK.P
Retrocopy PDP*SSVP-PS>APPSKKSLGTQAPKKAVEKKQPSESSEDSSDESDSSLEEEDE<TLAKSVISKANTKQP

Parental  PAKKAAESSSDSSDSDSSEDDEAPSKPAGTTKNSSNKPAVTTKSPAVKPAAAPKQPVGGGQKLLTRKADS
          PAKKAAESSSDSS.S.SSEDDEA.SK.A.T.KNSSNKPA.TTKSPA..PAA..KQP...GQK.L.RKADS
Retrocopy PAKKAAESSSDSSYSNSSEDDEALSKLASTSKNSSNKPAATTKSPATEPAATLKQPASSGQKPLMRKADS

Parental  SSSEEESSSSEEEKTKKMVATTKPKATAKAAPPLPAKQAPQGSRDSSSDSDSSSS--EEEEEKTSKSAVK
          .SSE.ESSSSEEEKTK..V...KPK.T.KAAP.LPAKQAP..S.DSSS.SDSSSS..EEEEEKTSKS.VK
Retrocopy NSSEKESSSSEEEKTKMTVDPLKPKVTDKAAPYLPAKQAPERSKDSSSHSDSSSSEEEEEEEKTSKSPVK

Parental  KKPQKVAGGAAPSKPASAKKGKAESSSSSSSDDSSEEEEEKPKGKGSPRPQAPKANGTSALTAQNGKAAK
          KK.QK.AGG.APSKPAS.KKGK..SSS.SSSDDSSEEEE.KPKGK.SPRPQ.PKANGTSALTAQNGKAAK
Retrocopy KKLQKAAGGTAPSKPASTKKGKVKSSSNSSSDDSSEEEEAKPKGKDSPRPQVPKANGTSALTAQNGKAAK

Parental  NSE--EEEEEKKK-AAVVVSKSGSLKKRKQ-NEAAKEAETPQAKKIKLQTPNTFPKRKKGEKRASSPFRR
          NSE.......KKK.AAVVVSK.GS.KK.KQ..E.AKEAETP.AKKIKLQTPNTFPKRKK.EKRA.S.F.R
Retrocopy NSEXXXXXXXKKKKAAVVVSKLGSGKKWKQ<AETAKEAETPPAKKIKLQTPNTFPKRKKEEKRA*STFLR

Parental  VREEEIEVDSRVADNSFDAKRGAAGDW-GERANQVLKFTKGKSFRHEKTKKKRGSYRGGSISVQVNSIKF
          VREEEI......ADNS.DA..GAAGDW.GERAN.VL.FTKGKSF..EKTKK...S...GSISVQVNSI.F
Retrocopy VREEEIQ----AADNSIDAN*GAAGDW<GERANEVLRFTKGKSFWYEKTKKQGISWE-GSISVQVNSINF

Parental  DSE
          .SE
Retrocopy ESE

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	36.57 RPM
SRP007412_cerebellum	0.00 RPM	81.41 RPM
SRP007412_heart	0.00 RPM	25.12 RPM
SRP007412_kidney	0.00 RPM	29.05 RPM
SRP007412_liver	0.00 RPM	63.50 RPM
SRP007412_testis	0.00 RPM	35.30 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3182 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3182 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010062	1 retrocopy	retro_cfam_1047,
Callithrix jacchus	ENSCJAG00000017832	2 retrocopies	retro_cjac_4136, retro_cjac_4187,
Homo sapiens	ENSG00000166197	1 retrocopy	retro_hsap_4781,
Nomascus leucogenys	ENSNLEG00000015012	1 retrocopy	retro_nleu_1101,
Pongo abelii	ENSPPYG00000002595	1 retrocopy	retro_pabe_3721,
Pan troglodytes	ENSPTRG00000023882	1 retrocopy	retro_ptro_3182 ,
Tursiops truncatus	ENSTTRG00000014974	1 retrocopy	retro_ttru_155,