RetrogeneDB ID: retro_ptro_1372

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:44480426..44480708(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPX1
• Ensembl ID: ENSPTRG00000024355
• Aliases: None
• Description: Pan troglodytes selenoprotein X, 1 (SEPX1), mRNA. [Source:RefSeq mRNA;Acc:NM_001114751]

Sequence

>retro_ptro_1372
ATGTCATTCTGCAGCTTCTTCGGGGGCAAGGTTTTCCAGAATCACTTTGAGCCAGGCGTCTATATGTGTGCCAACTGTGG
CTATGAGCTGTTCCCCAGCCACTCAAAGTACACATACTCATTCCCCTGGCCGGTGTTCACCAAGACCATCCGTTCTGACA
GCGTGGCCAAGCGCCCAGAGCACAATCATCCTGAAGTCTTGAAGGTGTCTTGTGGCAAGTGTGGCAACACGTTGAGCCAC
AAGTTCCTGAACGATGGCCCCAAGCTGCGGCAGTCCCGATTC

Alignment

ORF - retro_ptro_1372 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.79 %
• Parental protein coverage: 83.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSFCSFFGGEVFQNHFEPGVYVCAKCGYELFSSCSKYAHSSPWPAFTETIHADSVAKRPEHNRPEALKVS
          MSFCSFFGG.VFQNHFEPGVY.CA.CGYELF.S.SKY..S.PWP.FT.TI..DSVAKRPEHN.PE.LKVS
Retrocopy MSFCSFFGGKVFQNHFEPGVYMCANCGYELFPSHSKYTYSFPWPVFTKTIRSDSVAKRPEHNHPEVLKVS

Parental  CGKCGNGLGHEFLNDGPKPGQSRF
          CGKCGN.L.H.FLNDGPK..QSRF
Retrocopy CGKCGNTLSHKFLNDGPKLRQSRF

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	2.79 RPM
SRP007412_cerebellum	0.00 RPM	1.86 RPM
SRP007412_heart	0.00 RPM	3.00 RPM
SRP007412_kidney	0.00 RPM	31.98 RPM
SRP007412_liver	0.00 RPM	40.46 RPM
SRP007412_testis	0.00 RPM	2.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1372 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1372 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2057

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008487	1 retrocopy	retro_amel_1468,
Homo sapiens	ENSG00000198736	1 retrocopy	retro_hsap_2057,
Microcebus murinus	ENSMICG00000011349	1 retrocopy	retro_mmur_1267,
Macaca mulatta	ENSMMUG00000007936	1 retrocopy	retro_mmul_1402,
Pan troglodytes	ENSPTRG00000024355	1 retrocopy	retro_ptro_1372 ,