RetrogeneDB ID: retro_ptro_2671

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:5815016..5815968(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TADA1
• Ensembl ID: ENSPTRG00000001627
• Aliases: TADA1, TADA1L
• Description: None

Sequence

>retro_ptro_2671
ATGGCAACCTTTGTGAGTGAGCTGGAGGTGGCCAAGAAGAACTTGAGTGAGGCCCTGGGGGACAACATGAATCAATACTG
GCCTAACTTAAGCTGTGGTTCAAGCGGAAGATCAGGAAAGAGGACTTTGACCTTGAAACTCATAGGCTTCTTACATAGGA
TAATATGCATTCTCACAATGATTTCCTCCTGGACATTCTCACGCATTGTCAGATTTTGGTTTCTACATCAGAGGGTGCTG
GATCTTTGCCCTGGATTGGGGGTTCCGCAGCAAAACCTGGAAAGCCCAATGGAAAGAAAAAGCTTTCTTCTGTCCGAAAT
TTGATTATAGATTCCAGCCTCACAATCCTTTCTCAAGAGCCCAGTAATTTGTGGGAAAACATCCCCAAGATGATGATGAC
TTGAAACTTTGTTCCCACACAATGATGCTTCTCATTCAAGGCTGGCTTGAAGGGAGAATGTCAGTGACTGCTTATGAGCA
TGGGCTGGACAATGTCACCGAGGAGGCTATTTCAGCTCTTGTCTATGCTTTGGAGAATCACCCTAAAGATATACTGACAT
CAGTTGTGTCAAGAAGGAAAGCTTATCAGTTATGAGATGACCATTTTAAATATGCCTTTGGCAGTAATGTGACCCCATAG
CCATACCTGAAGAATAATGTAGTAGCTTAGAACAACTTAATATAAAGCCCTCAAGCTTTTACTGCTCCTTGTGCTGGTCA
GAATCCAGCTTCTCACCCACCTCCTGATGAAGCCGAGCAGCAGGCTACATTCCTGCTGGCATGCTCTGGAGACACTCTAT
CTGCATCTTTATCTCCAGTGAACATGTATGAACTTTTTGAAGCTCTGTGCGTACACAGGGAAGTCATACCTACACATACT
GTCTATGCCGTTAACATTGAAAGGATCATCATGAAAGTCTGGCATCCAAATCATGAAGAGCTGAAGACAGAG

Alignment

ORF - retro_ptro_2671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.06 %
• Parental protein coverage: 95.22 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATFVSELEAAKKNLSEALGDNVKQYWANL-KLWFKQKISKEEFDLEAHRLLTQDNVHSHNDFLLAILTR
          MATFVSELE.AKKNLSEALGDN..QYW.NL.KLWFK.KI.KE.FDLE.HRLLT.DN.HSHNDFLL.ILT.
Retrocopy MATFVSELEVAKKNLSEALGDNMNQYWPNL<KLWFKRKIRKEDFDLETHRLLT*DNMHSHNDFLLDILTH

Parental  CQILVSTPDGAGSLPWPGGSAAKPG-KPKGKKKLSSVRQKFDHRFQPQNPLSGAQQFVAKDPQDDDDLKL
          CQILVST..GAGSLPW.GGSAAKPG.K...K.K......KFD.RFQP.NP.S.AQ.FV.K.PQDDDDLKL
Retrocopy CQILVSTSEGAGSLPWIGGSAAKPG<KAQWKEK-AFFCPKFDYRFQPHNPFSRAQ*FVGKHPQDDDDLKL

Parental  CSHTMMLPTRGQLEGRMIVTAYEHGLDNVTEEAVSAVVYAVENHLKDILTSVVSRRKAYRLRDGHFKYAF
          CSHTMML...G.LEGRM.VTAYEHGLDNVTEEA.SA.VYA.ENH.KDILTSVVSRRKAY.L.D.HFKYAF
Retrocopy CSHTMMLLIQGWLEGRMSVTAYEHGLDNVTEEAISALVYALENHPKDILTSVVSRRKAYQL*DDHFKYAF

Parental  GSNVTPQPYLKNSVVAYNNLIESPPAFTAPCAGQNPASHPPPDDAEQQAALLLACSGDTLPASLPPVNMY
          GSNVTP.PYLKN.VVA.NNLI.SP.AFTAPCAGQNPASHPPPD.AEQQA..LLACSGDTL.ASL.PVNMY
Retrocopy GSNVTP*PYLKNNVVA*NNLI*SPQAFTAPCAGQNPASHPPPDEAEQQATFLLACSGDTLSASLSPVNMY

Parental  DLFEALQVHREVIPTHTVYALNIERIITKLWHPNHEELQQD
          .LFEAL.VHREVIPTHTVYA.NIERII.K.WHPNHEEL...
Retrocopy ELFEALCVHREVIPTHTVYAVNIERIIMKVWHPNHEELKTE

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	11.74 RPM
SRP007412_cerebellum	0.00 RPM	14.45 RPM
SRP007412_heart	0.00 RPM	4.75 RPM
SRP007412_kidney	0.00 RPM	8.63 RPM
SRP007412_liver	0.00 RPM	6.71 RPM
SRP007412_testis	0.00 RPM	7.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2671 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2671 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2671 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3928
Gorilla gorilla	retro_ggor_2644
Pongo abelii	retro_pabe_3243

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015607	1 retrocopy	retro_cfam_849,
Choloepus hoffmanni	ENSCHOG00000012658	1 retrocopy	retro_chof_602,
Cavia porcellus	ENSCPOG00000025598	1 retrocopy	retro_cpor_1225,
Dasypus novemcinctus	ENSDNOG00000018606	1 retrocopy	retro_dnov_1293,
Homo sapiens	ENSG00000152382	1 retrocopy	retro_hsap_3928,
Gorilla gorilla	ENSGGOG00000008168	1 retrocopy	retro_ggor_2644,
Mus musculus	ENSMUSG00000026563	1 retrocopy	retro_mmus_865,
Otolemur garnettii	ENSOGAG00000007621	1 retrocopy	retro_ogar_1989,
Pongo abelii	ENSPPYG00000000557	1 retrocopy	retro_pabe_3243,
Pan troglodytes	ENSPTRG00000001627	1 retrocopy	retro_ptro_2671 ,
Tupaia belangeri	ENSTBEG00000007283	1 retrocopy	retro_tbel_3501,