RetrogeneDB ID: retro_ptro_352

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:148784831..148785466(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAUS4
• Ensembl ID: ENSPTRG00000006153
• Aliases: None
• Description: None

Sequence

>retro_ptro_352
AAGGCATGGAAGGAAGTTCGACTGCATAAGACAACGTGGTTGAGGTCTGAGATTTTACATGGAGTTATTCAGGAGTTGCT
TGTGGACTACTGTGTGAAGATACAGGACACAAATTTAACTTCTGAGGACAAAAATTTCATGAGACTCTTGAACAGCGGCT
ACTCATAACTGAACTGATATGGCTCTTAGGTCCTAGCCAGGAGAGGGAGATACCTTCACTGCTAGAGCTGGAGAAAGCAG
ACCTTCTGGAATCCATGCCACTCTCAGACGATTTTGTGTGGATGAGGGCTCTGCTACAGCAAGAAGTGGAGGAGTAGCTC
AAGAAGAAATGTTTCACTCTGCTCTGGTACTATGATCCCAATTCAGATGCTGACAGTGAAACCGTGAAGGCAGCAAACGT
GTTGAAACTTGCAGAGGTCCTAGTGGCTAGGAAGCAGCAGTGCCAGGATGCCAAGAGCCAGCAAAAGGAGCAGATGGTGC
TGCTGGAGAAGAAGAGTGCCACCTACTTCCAGGTGCTTCTCTGCTGCCTCATTTTGCTGCAGAGGCTTCTTCAGGAACAA
CGGCTGAAGACTCACTCCGAGTTAGACCACATCAATGCCCAGTACCTGGAAGTCAAGTGTGGTGCTATGATACTT

Alignment

ORF - retro_ptro_352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.92 %
• Parental protein coverage: 58.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QAWKEVRLHKTTWLRSEILHRVIQELLVDYYVKIQDTNVTSEDK-KFHETLEQRLLVTELMRLLGPSQER
          .AWKEVRLHKTTWLRSEILH.VIQELLVDY.VKIQDTN.TSEDK.KFHETLEQRLL.TEL..LLGPSQER
Retrocopy KAWKEVRLHKTTWLRSEILHGVIQELLVDYCVKIQDTNLTSEDK<KFHETLEQRLLITELIWLLGPSQER

Parental  EIPPLLGLEKADLLELMPLSEDFVWMRARLQQEVEEQLKKKCFTLLCYCDPNSDADSETVKAAKVWKLTE
          EIP.LL.LEKADLLE.MPLS.DFVWMRA.LQQEVEE.LKKKCFTLL.Y.DPNSDADSETVKAA.V.KL.E
Retrocopy EIPSLLELEKADLLESMPLSDDFVWMRALLQQEVEE*LKKKCFTLLWYYDPNSDADSETVKAANVLKLAE

Parental  VLVGEQQQCQDAKSQQKEQMLLLEKKSAAYSQVLLRCLTLLQRLLQEHRLKTQSELDRINAQYLEVKCGA
          VLV...QQCQDAKSQQKEQM.LLEKKSA.Y.QVLL.CL.LLQRLLQE.RLKT.SELD.INAQYLEVKCGA
Retrocopy VLVARKQQCQDAKSQQKEQMVLLEKKSATYFQVLLCCLILLQRLLQEQRLKTHSELDHINAQYLEVKCGA

Parental  MIL
          MIL
Retrocopy MIL

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	7.81 RPM
SRP007412_cerebellum	0.18 RPM	14.45 RPM
SRP007412_heart	0.06 RPM	7.34 RPM
SRP007412_kidney	0.08 RPM	22.46 RPM
SRP007412_liver	0.00 RPM	7.43 RPM
SRP007412_testis	0.00 RPM	14.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_352 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_352 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_352 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_469
Gorilla gorilla	retro_ggor_447
Pongo abelii	retro_pabe_265

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008389	1 retrocopy	retro_cjac_757,
Dasypus novemcinctus	ENSDNOG00000002575	1 retrocopy	retro_dnov_712,
Homo sapiens	ENSG00000092036	1 retrocopy	retro_hsap_469,
Gorilla gorilla	ENSGGOG00000007504	1 retrocopy	retro_ggor_447,
Myotis lucifugus	ENSMLUG00000012934	1 retrocopy	retro_mluc_1946,
Otolemur garnettii	ENSOGAG00000000586	1 retrocopy	retro_ogar_382,
Pongo abelii	ENSPPYG00000005651	1 retrocopy	retro_pabe_265,
Pan troglodytes	ENSPTRG00000006153	1 retrocopy	retro_ptro_352 ,