RetrogeneDB ID: retro_mmul_177

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214474519:1..445(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000029023
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TFDP1
• Ensembl ID: ENSMMUG00000007423
• Aliases: None
• Description: None

Sequence

>retro_mmul_177
ATGGCAAAAGATGCCGGTTTAATTGAAGCCAACGGAGAACTCAAGGTCTTCATAGATCAGAACCTTAGTCCCGGGAAAGG
CGTGGTGTCCCTTGTGGCCGTTCACCCCTCCACAGTCAACCCGCTCGGGAAGCAGCTTTTGCCAAAAGCCTTTGGACCGT
CCAATGTCAGCATTGCCCAGCAAGTGGTGATTGGTATGCCTCAGAGACCTGCAGCGTCAAACAGCCTGGTGGTAGGAAGC
CCACACCCCCCCAGCACTCACTTTGCCTCTCAGAACCAGCCTTCTGACTCCTCACCTCGGTTTGCAGGGAAGCGCATCAG
GAAGGGAGAGAATTGCAAGGGCCTGCGGCATTTCTCCATGAAGGTCTGCGAGAAGGTGCAGAGGAAGGGGACCACTTCCT
ACAACGAAGTGGCGGACGAGCTGGTTGCAGAGTTCAGTGCTGCC

Alignment

ORF - retro_mmul_177 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.41 %
• Parental protein coverage: 61.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGLIEANGELKVFIDQNLSPGKGVVSLVAVHPSTVNPLGKQLLPKTFGQSNVNIAQQVVIGTPQRPAASN
          AGLIEANGELKVFIDQNLSPGKGVVSLVAVHPSTVNPLGKQLLPK.FG.SNV.IAQQVVIG.PQRPAASN
Retrocopy AGLIEANGELKVFIDQNLSPGKGVVSLVAVHPSTVNPLGKQLLPKAFGPSNVSIAQQVVIGMPQRPAASN

Parental  TLVVGSPHTPSTHFASQNQPSDSSPWSAGKRNRKGEKNGKGLRHFSMKVCEKVQRKGTTSYNEVADELVA
          .LVVGSPH.PSTHFASQNQPSDSSP..AGKR.RKGE.N.KGLRHFSMKVCEKVQRKGTTSYNEVADELVA
Retrocopy SLVVGSPHPPSTHFASQNQPSDSSPRFAGKRIRKGE-NCKGLRHFSMKVCEKVQRKGTTSYNEVADELVA

Parental  EFSAA
          EFSAA
Retrocopy EFSAA

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	0.00 RPM	16.14 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	29.19 RPM
SRP007412_cerebellum	0.00 RPM	29.38 RPM
SRP007412_heart	0.00 RPM	15.25 RPM
SRP007412_kidney	0.00 RPM	19.95 RPM
SRP007412_liver	0.00 RPM	13.18 RPM
SRP007412_testis	0.00 RPM	37.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_177 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_177 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004467	8 retrocopies	retro_chof_2187, retro_chof_2229, retro_chof_2621, retro_chof_506, retro_chof_529, retro_chof_837, retro_chof_854, retro_chof_895,
Callithrix jacchus	ENSCJAG00000006950	2 retrocopies	retro_cjac_179, retro_cjac_4094,
Homo sapiens	ENSG00000198176	4 retrocopies	retro_hsap_1601, retro_hsap_299, retro_hsap_4803, retro_hsap_61,
Gorilla gorilla	ENSGGOG00000004908	2 retrocopies	retro_ggor_17, retro_ggor_335,
Loxodonta africana	ENSLAFG00000007927	1 retrocopy	retro_lafr_914,
Myotis lucifugus	ENSMLUG00000012165	1 retrocopy	retro_mluc_896,
Macaca mulatta	ENSMMUG00000007423	1 retrocopy	retro_mmul_177 ,
Mus musculus	ENSMUSG00000038482	2 retrocopies	retro_mmus_3243, retro_mmus_338,
Nomascus leucogenys	ENSNLEG00000000849	3 retrocopies	retro_nleu_2177, retro_nleu_2598, retro_nleu_49,
Otolemur garnettii	ENSOGAG00000003532	1 retrocopy	retro_ogar_3334,
Pongo abelii	ENSPPYG00000025889	3 retrocopies	retro_pabe_1314, retro_pabe_132, retro_pabe_378,