RetrogeneDB ID: retro_ptro_1897

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:71401980..71403528(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNPC3
• Ensembl ID: ENSPTRG00000033902
• Aliases: None
• Description: None

Sequence

>retro_ptro_1897
ATGCCAGCTCTCTATCAGCCATTTGCAATATCAAGGGGATGCACAAGCTCCTCCTCACTTTCCCTGCCTCGGCCGACCGA
ACCCTTCTGGTGAGGCACCTGCCAGCTGAGCTGACCGCTGAGGAGAAAGAGGACTTGCTGAAGTACTTCAAGGCACAGTT
GGTGCATGACCTGTCAGATAAGGGGCAGCTGAAACATACAGCTTTTGCCACATTCCCTAAAAAGCAGCTATAAAGGCATT
GACAAGACTCCATCAGCTGAAACTTTTAGGTCATACTTTAGTCTTTGAATTTGCAAAAGAGCAGGATCAAGTTCACCCCC
CATGTCCCACTTCAGTCTCTGAAAAAAAAAAAAAAAAAAGGTCTGATGACCCTGTTGAAGACGATAAAGAAAAGAAAGAA
TTTGGTTATTTAACAGTAGAAAATGGAATTACACCAAACCATGGGCTCACTTTTCTTAATTCATGCCTCAAGTATATGTA
CCCACCACCTTCCAGCACAATCCTAGCAAACAGAGTAAATGCTTTGGCAAGCATGCCTAAGTTCTATGTACAGGTCCTTC
ATCTTATGAATAAAATGAATTTGCCCACAGCTTTTAGATCAATTACTGCACGGCCTCCCATCTCTGAAGACCATATGCCA
TTGCATCCACCTCTTCCACCCACATCTCCTCAGCCACCTGAGGAACCTCCTTGGCCAGAAGACGATGAGGAATTATCTAG
TGAAGAATTAGAAGATGACAGCAGTGATGATGAGGACCAACAGAGAATGAACAAACTAATGGAACTAGCAAATCTTCAGC
CCCAAAGACCCAAAGCAATAAGGCAGCGCCATGTGAGAAAAAAGAGAAAAATAAAGGATATGCTGAACATACTTTCGTGT
CCTTCACAAAACAGTTTACATCTAGTGCTGTTACCTTCGGATGTATTTGACCAACCACAATCTGTAGGTAATAAAAGAAT
TGAATTCCATATATCTACCGACATGCCAGCTGCATTTAAGAAAGATTTAGAGAAGAAAGAAAATTGTGAGAAAAAAATAA
TGATCTACCTGTTACTGAAGCTGATGCATCCAGTATAGGATTTGGAAAAATCTTTCCCAAACCTAATTTGAACATCACAG
AAGAGATTAAAAAAGACTCTGATGAAATGCCATCGGAATGTATTTCTAGAAGGGAATTGGAAAAGGACAGAATTTCTAGA
GAAGAAATGGAAACACTTTCAGTTTTCAGAAGTTATGAACCTGGTGAACCAAACTGTAGAATTTATGTAAAGAATTTAGC
TAAACATGTTCAAGAAAAGGACCTTAAATATATTTTTGGAAGATATGTTGACTTTTCATCAGAAACACAGTAGATCATGT
TTGATATATGTTTGATGAAAGAAGGTCGTATGAAAGGACAAGCTTCCATTGGACTTCCTAATGAAAAAGCAGCAGCAAAA
GCCTTAAAGGAAGCTAATGGATATGTGCTTTTTGGAAAACCCATGGTGGTTCAATTTGCTCGATCTGCTAGACAAAAACC
AGATCCTAAGGAAGGAAAAAGAAAATGT

Alignment

ORF - retro_ptro_1897 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAPEQPLAISRGCTSSSSLSPPR-GDRTLLVRHLPAELTAEEKEDLLKYFGAQSVRVLSDKGRLKHT-A
          M.A..QP.AISRGCTSSSSLS.PR..DRTLLVRHLPAELTAEEKEDLLKYF.AQ.V..LSDKG.LKHT..
Retrocopy MPALYQPFAISRGCTSSSSLSLPR<ADRTLLVRHLPAELTAEEKEDLLKYFKAQLVHDLSDKGQLKHT<S

Parental  FATFPNEKAAIKALTRLHQLKLLGHTLVVEFAKEQDRVHSPCPTSGSEKKKR--SDDPVEDDKEKKELGY
          F...P..KAAIKALTRLHQLKLLGHTLV.EFAKEQD.VH.PCPTS.S.......SDDPVEDDKEKKE.GY
Retrocopy FCHIP*-KAAIKALTRLHQLKLLGHTLVFEFAKEQDQVHPPCPTSVSXXXXXXXSDDPVEDDKEKKEFGY

Parental  LTVENGIAPNHGLTFPLNSCLKYMYPPPSSTILANIVNALASVPKFYVQVLHLMNKMNLPTPFGPITVRP
          LTVENGI.PNHGLTF.LNSCLKYMYPPPSSTILAN.VNALAS.PKFYVQVLHLMNKMNLPT.F..IT.RP
Retrocopy LTVENGITPNHGLTF-LNSCLKYMYPPPSSTILANRVNALASMPKFYVQVLHLMNKMNLPTAFRSITARP

Parental  PMYEDYMPLHAPLPPTSPQPPEEPPLPDEDEELSSEESEYESTDDEDRQRMNKLMELANLQPKRPKTIKQ
          P..ED.MPLH.PLPPTSPQPPEEPP.P..DEELSSEE.E..S.DDED.QRMNKLMELANLQP.RPK.I.Q
Retrocopy PISEDHMPLHPPLPPTSPQPPEEPPWPEDDEELSSEELEDDSSDDEDQQRMNKLMELANLQPQRPKAIRQ

Parental  RHVRKKRKIKDMLNTPLCPSHSSLHPVLLPSDVFDQPQPVGNKRIEFHISTDMPAAFKKDLEKEQNCE-E
          RHVRKKRKIKDMLN...CPS..SLH.VLLPSDVFDQPQ.VGNKRIEFHISTDMPAAFKKDLEK..NCE.E
Retrocopy RHVRKKRKIKDMLNILSCPSQNSLHLVLLPSDVFDQPQSVGNKRIEFHISTDMPAAFKKDLEKKENCE<E

Parental  KNHDLPATEVDASNIGFGKIFPKPNLDITEEIKEDSDEMPSECISRRELEKGRISREEMETLSVFRSYEP
          KN.DLP.TE.DAS.IGFGKIFPKPNL.ITEEIK.DSDEMPSECISRRELEK.RISREEMETLSVFRSYEP
Retrocopy KNNDLPVTEADASSIGFGKIFPKPNLNITEEIKKDSDEMPSECISRRELEKDRISREEMETLSVFRSYEP

Parental  GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKE
          GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQ.IMFDI.LMKEGRMKGQA.IGLPNEKAAAKALKE
Retrocopy GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQ*IMFDICLMKEGRMKGQASIGLPNEKAAAKALKE

Parental  ANGYVLFGKPMVVQFARSARPKQDPKEGKRKC
          ANGYVLFGKPMVVQFARSAR.K.DPKEGKRKC
Retrocopy ANGYVLFGKPMVVQFARSARQKPDPKEGKRKC

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	0.04 RPM	17.70 RPM
SRP007412_cerebellum	0.00 RPM	45.71 RPM
SRP007412_heart	0.06 RPM	16.23 RPM
SRP007412_kidney	0.05 RPM	25.84 RPM
SRP007412_liver	0.00 RPM	9.82 RPM
SRP007412_testis	0.00 RPM	16.12 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1897 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1897 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1897 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2800
Pongo abelii	retro_pabe_2224
Macaca mulatta	retro_mmul_1435
Callithrix jacchus	retro_cjac_1397

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000035686	1 retrocopy	retro_cjac_1397,
Homo sapiens	ENSG00000185946	1 retrocopy	retro_hsap_2800,
Macaca mulatta	ENSMMUG00000018039	1 retrocopy	retro_mmul_1435,
Nomascus leucogenys	ENSNLEG00000012013	1 retrocopy	retro_nleu_1539,
Nomascus leucogenys	ENSNLEG00000015566	1 retrocopy	retro_nleu_1538,
Pongo abelii	ENSPPYG00000001102	1 retrocopy	retro_pabe_2224,
Pan troglodytes	ENSPTRG00000033902	1 retrocopy	retro_ptro_1897 ,