RetrogeneDB ID: retro_ptro_2141

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:36528820..36529436(+)
• Located in intron of: ENSPTRG00000017020

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPACT
• Ensembl ID: ENSPTRG00000009927
• Aliases: None
• Description: None

Sequence

>retro_ptro_2141
CAGAATATTGGTGAAAGTATTCTTTACCTGTGAGTGGAGAAAATAAGAGATGTTCCAATACAAAAACCTCAGATGACAGA
ACCAGGCCCAGAGGTAAAGAAAGAAACTGAAGAGGAAGATGTTGAATGTGAAGATGATCTCATTTTTGCATGTCAGCCAG
AAAGTTCGGTGAAAGCACTGGATTTTGATATCAGTGAAAATCAAAGAGAAATAGAATTATCTCTGATTGATCATGGCATT
TCTGTTACAGACCGAATAAGTACTTTTCAGGCAGACTTTGATCCAGCAGTTTGTCCCAAACAGGTGAAAATGGTTCTTTC
CAACTTGTATGAGAATAAGAAAATAGCTAGTACCACCCACAGCATCTATGCCTACAGAGTGTATTGTGAGAATAAACAGA
CCTTCTTACAGGATTGTGAGGATGATGGGGAAAGAGCAGCTGGTGGGCATCTTCTTCATCTCATGGAGATTTTAAATGTG
AGGAATATCATGGTGGTGGTATCACGCTGGTATGGAGGGATTCTGTAGGACCAGATCACTTTAAACATAACTGTGCCAGA
AACATACTAGTGGAGAAGAACAACACACATTCACCTGAAAATCATCTAAGGCTTTG

Alignment

ORF - retro_ptro_2141 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.75 %
• Parental protein coverage: 65.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QNIGESILYLWVEKIRDVLIQKSQMTEPGSDVKKKTEEEDVECEDDLILACQPESSVKALDFDISETRTE
          QNIGESILYL.VEKIRDV.IQK.QMTEPG..VKK.TEEEDVECEDDLI.ACQPESSVKALDFDISE...E
Retrocopy QNIGESILYL*VEKIRDVPIQKPQMTEPGPEVKKETEEEDVECEDDLIFACQPESSVKALDFDISENQRE

Parental  VEVEELPPIDHGIPITDRRSTFQAHLAPVVCPKQVKMVLSKLYENKKIASATHNIYAYRIYCEDKQTFLQ
          ....EL..IDHGI..TDR.STFQA...P.VCPKQVKMVLS.LYENKKIAS.TH.IYAYR.YCE.KQTFLQ
Retrocopy I---ELSLIDHGISVTDRISTFQADFDPAVCPKQVKMVLSNLYENKKIASTTHSIYAYRVYCENKQTFLQ

Parental  DCEDDGETAAGGRLLHLMEILNVKNVMVVVSRWYGGIL-LGPDRFKHINNCARNILVEKNYTNSPE-ESS
          DCEDDGE.AAGG.LLHLMEILNV.N.MVVVSRWYGGIL..GPD.FKH..NCARNILVEKN.T.SPE..SS
Retrocopy DCEDDGERAAGGHLLHLMEILNVRNIMVVVSRWYGGIL<VGPDHFKH--NCARNILVEKNNTHSPE<KSS

Parental  KAL
          KAL
Retrocopy KAL

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	0.02 RPM	2.70 RPM
SRP007412_cerebellum	0.00 RPM	4.84 RPM
SRP007412_heart	0.03 RPM	9.27 RPM
SRP007412_kidney	0.31 RPM	8.11 RPM
SRP007412_liver	0.13 RPM	4.88 RPM
SRP007412_testis	0.32 RPM	34.78 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2141 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2141 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2141 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3341
Pongo abelii	retro_pabe_2753

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013068	1 retrocopy	retro_chof_2523,
Erinaceus europaeus	ENSEEUG00000003962	1 retrocopy	retro_eeur_409,
Homo sapiens	ENSG00000154059	1 retrocopy	retro_hsap_3341,
Macaca mulatta	ENSMMUG00000004664	1 retrocopy	retro_mmul_1041,
Nomascus leucogenys	ENSNLEG00000006582	1 retrocopy	retro_nleu_1166,
Pongo abelii	ENSPPYG00000009071	1 retrocopy	retro_pabe_2753,
Pan troglodytes	ENSPTRG00000009927	1 retrocopy	retro_ptro_2141 ,
Sorex araneus	ENSSARG00000002836	1 retrocopy	retro_sara_719,