RetrogeneDB ID: retro_mmul_48

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:56376428..56377034(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000002180
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.4252
• Ensembl ID: ENSMMUG00000014661
• Aliases: None
• Description: None

Sequence

>retro_mmul_48
ATGGCGGCGCGGACAGCGTTCGGGGCCGTGTGCCGGCGCCTCTGGCAGGGATTGGGGAATTTTTCTGTAAACAGTTCTAA
GGGCGATACAGTCAAAAATGGTGGCTTTCTTCTCAGTACCAATATGAAGTGGGTACAGTTTTCAAACCTACATGTTGATG
TTCCAAAGGATTTGACCAAACCTGTGATAACGATCTCTGATGAACCAGATACATTATATAAGCGCCTGTCGGTTTTAGTG
AAAGGTCACGATAAGGCTGTATTGGACAGTTATGAATATTTTGCTGTGCTTGCTGCAAAAGAACTTGGTATCTCTATTAA
AGTACACGAACCTCCAAGGAAAATAGAGCGATTTACTCTTCTCAAATCAGTGCATATTTACAAGAAGCACAGAGTTCAGT
ATGAAATGAGAACACTTTACAGATGTTTAGAGTTAGAACATCTAACTGGAAGCACAGCAGATGTCTACTTGGAATACATT
CAGCGAAACTTACCTGAAGGGGTTGCCATGGAAGTAACAAAGACACAGTTAGAACAGTTACCAGAACACATCAAGGAGCC
AATCTGGGAAACACTATCAGAAGAAAAAGAAGAAAGCAAGTCATAA

Alignment

ORF - retro_mmul_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.01 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAARTAFGAVCRRLWQGLGNFSVNSSKGDTVKNGGFLLHSSTNMKWVQFSNLHVDVPKDLTKPVITISDE
          MAARTAFGAVCRRLWQGLGNFSVNSSKGDTVKNGGFLL..STNMKWVQFSNLHVDVPKDLTKPVITISDE
Retrocopy MAARTAFGAVCRRLWQGLGNFSVNSSKGDTVKNGGFLL--STNMKWVQFSNLHVDVPKDLTKPVITISDE

Parental  PDTLYKRLSVLVKGHDKAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTLLKSVHIYKKHRVQYEMRT
          PDTLYKRLSVLVKGHDKAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTLLKSVHIYKKHRVQYEMRT
Retrocopy PDTLYKRLSVLVKGHDKAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTLLKSVHIYKKHRVQYEMRT

Parental  LYRCLELEHLTGSTADVYLEYIQRNLPEGVAMEVTKTQLEQLPEHIKEPIWETLSEEKEESKS
          LYRCLELEHLTGSTADVYLEYIQRNLPEGVAMEVTKTQLEQLPEHIKEPIWETLSEEKEESKS
Retrocopy LYRCLELEHLTGSTADVYLEYIQRNLPEGVAMEVTKTQLEQLPEHIKEPIWETLSEEKEESKS

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	1.46 RPM	2.24 RPM
SRP007412_brain_prefrontal_cortex	1.82 RPM	3.65 RPM
SRP007412_cerebellum	0.97 RPM	1.42 RPM
SRP007412_heart	1.83 RPM	1.88 RPM
SRP007412_kidney	0.82 RPM	2.00 RPM
SRP007412_liver	0.51 RPM	1.43 RPM
SRP007412_testis	1.55 RPM	0.90 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_48 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_48 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_48 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001638	1 retrocopy	retro_cfam_598,
Choloepus hoffmanni	ENSCHOG00000006109	1 retrocopy	retro_chof_1964,
Dasypus novemcinctus	ENSDNOG00000006067	1 retrocopy	retro_dnov_2007,
Dipodomys ordii	ENSDORG00000002081	1 retrocopy	retro_dord_412,
Homo sapiens	ENSG00000048544	1 retrocopy	retro_hsap_4157,
Gorilla gorilla	ENSGGOG00000012808	1 retrocopy	retro_ggor_2532,
Microcebus murinus	ENSMICG00000011379	1 retrocopy	retro_mmur_321,
Macaca mulatta	ENSMMUG00000014661	1 retrocopy	retro_mmul_48 ,
Mus musculus	ENSMUSG00000034729	1 retrocopy	retro_mmus_1654,
Nomascus leucogenys	ENSNLEG00000004800	1 retrocopy	retro_nleu_1385,
Oryctolagus cuniculus	ENSOCUG00000016697	1 retrocopy	retro_ocun_1141,
Pongo abelii	ENSPPYG00000016613	1 retrocopy	retro_pabe_3456,
Pan troglodytes	ENSPTRG00000018169	1 retrocopy	retro_ptro_2826,
Rattus norvegicus	ENSRNOG00000022609	1 retrocopy	retro_rnor_2284,
Ictidomys tridecemlineatus	ENSSTOG00000027016	1 retrocopy	retro_itri_1183,
Tursiops truncatus	ENSTTRG00000014063	1 retrocopy	retro_ttru_1203,