RetrogeneDB ID: retro_ptro_145

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:51216839..51217089(+)
• Located in intron of: ENSPTRG00000000725

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC5A3
• Ensembl ID: ENSPTRG00000013877
• Aliases: None
• Description: None

Sequence

>retro_ptro_145
ATGCCCCACTATGAGCTGGCTTTAATCCTGAAAGCCATGCCGCGGCCAGACTGCTGCTGCTTTGAAACATACGATAGAGG
TTCTGATGGAAAAAGGAGCAATAGTGAGGAACTTGGAAAACCTGGGTGAGTGAGCGCTTCCTTGTGAGATCTCTACCCAC
AATCAGTGGCACAACAGAGGCGGGTATTTCCTGGTGAATTTTTATGCACCAACCACAACTGTTGAAAGCATGATGGAGCA
CTTCTCCAAA

Alignment

ORF - retro_ptro_145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.94 %
• Parental protein coverage: 67.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPRYELALILKAMQRPE-TAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNRGGYFLVDFY
          MP.YELALILKAM.RP...AA.LK.TIE.LM..GAIVR.LENLGE.ALP..IS.H.Q.HNRGGYFLV.FY
Retrocopy MPHYELALILKAMPRPD>AAA-LKHTIEVLMEKGAIVRNLENLGE*ALPCEISTHNQWHNRGGYFLVNFY

Parental  APTAAVESMVEHLSR
          APT..VESM.EH.S.
Retrocopy APTTTVESMMEHFSK

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	20.43 RPM
SRP007412_cerebellum	0.00 RPM	15.24 RPM
SRP007412_heart	0.00 RPM	12.04 RPM
SRP007412_kidney	0.00 RPM	36.66 RPM
SRP007412_liver	0.00 RPM	13.75 RPM
SRP007412_testis	0.00 RPM	35.20 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_145 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_145 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_145 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_149

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000025622	1 retrocopy	retro_dnov_498,
Homo sapiens	ENSG00000243927	1 retrocopy	retro_hsap_149,
Nomascus leucogenys	ENSNLEG00000004239	1 retrocopy	retro_nleu_896,
Pan troglodytes	ENSPTRG00000013877	1 retrocopy	retro_ptro_145 ,