RetrogeneDB ID: retro_ptro_481

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:38637840..38638125(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXYD6
• Ensembl ID: ENSPTRG00000004329
• Aliases: None
• Description: FXYD domain-containing ion transport regulator 6 precursor [Source:RefSeq peptide;Acc:NP_001230843]

Sequence

>retro_ptro_481
ATGGAGGTGGTGCTGATATTCCTATGCAGCCTGTTGGCCCTCATTGTCATGCCCAGTGCAGCTGAGTAGGAGAAGGAAAT
TGACCATTTTCATTATGACTAACAGACCCTGAGGATTCAGGGGTTGGTATGTGCTGTGGTCCTCTTCTCCGTTGGGATCT
TCCTTATCCTAGGTTGCAGATGCAAGTGGAGTTTCAATCAGAAGCCCGGGACCCCAGGGGAGGAGGAAGCCCAGGTGGAG
AACCTCATCACTGCAAATGCAGCAAAACTCCAGAAAGCAGAGAGC

Alignment

ORF - retro_ptro_481 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.79 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MELVLVFLCSLLAPTVLASAAEKEKEMDPFHYDYQTLRIGGLVFAVVLFSVGILLILSRRCKCSFNQKPR
          ME.VL.FLCSLLA..V..SAAE.EKE.D.FHYD.QTLRI.GLV.AVVLFSVGI.LIL..RCK.SFNQKP.
Retrocopy MEVVLIFLCSLLALIVMPSAAE*EKEIDHFHYD*QTLRIQGLVCAVVLFSVGIFLILGCRCKWSFNQKPG

Parental  APGDEEAQVENLITANATEPQKAEN
          .PG.EEAQVENLITANA...QKAE.
Retrocopy TPGEEEAQVENLITANAAKLQKAES

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	467.79 RPM
SRP007412_cerebellum	0.07 RPM	344.40 RPM
SRP007412_heart	0.00 RPM	32.18 RPM
SRP007412_kidney	0.00 RPM	96.97 RPM
SRP007412_liver	0.00 RPM	6.06 RPM
SRP007412_testis	0.00 RPM	43.10 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_481 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_481 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_481 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_662
Pongo abelii	retro_pabe_583
Pongo abelii	retro_pabe_648

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013044	1 retrocopy	retro_cjac_2098,
Erinaceus europaeus	ENSEEUG00000011989	1 retrocopy	retro_eeur_382,
Homo sapiens	ENSG00000137726	2 retrocopies	retro_hsap_562, retro_hsap_662,
Gorilla gorilla	ENSGGOG00000006473	2 retrocopies	retro_ggor_507, retro_ggor_574,
Macaca mulatta	ENSMMUG00000007617	2 retrocopies	retro_mmul_2439, retro_mmul_2440,
Nomascus leucogenys	ENSNLEG00000007348	2 retrocopies	retro_nleu_1982, retro_nleu_2890,
Pongo abelii	ENSPPYG00000003918	3 retrocopies	retro_pabe_583, retro_pabe_644, retro_pabe_648,
Pan troglodytes	ENSPTRG00000004329	3 retrocopies	retro_ptro_3127, retro_ptro_421, retro_ptro_481 ,