RetrogeneDB ID: retro_mmul_1471

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:146539018..146539298(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000019698
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.6747
• Ensembl ID: ENSMMUG00000011354
• Aliases: None
• Description: None

Sequence

>retro_mmul_1471
ATCTGTTTCTGCAAGCAGGCTGGTGTTGCCATCGGAAGATTGTGTGAAAACTGTGACAGCAAGCGTGTGATTTGTGACCG
CTGTGTGTGTCCCTGCACCCTGGTGTGCTTATGTGATGAGTGTAACAATGGCTCTTACCAGGGGCACTGTGAGATCTGTG
GAGGCCGTGGGAGTCTCTGATGCCTATTATTGTAAGGAGTGCACCAGCCAGGAGAAGGATAGAGATGGCTGCCCAAAGAT
TGTCAGCTTAGGGAGCTCTGAGACAGACCTCTTCCATGAA

Alignment

ORF - retro_mmul_1471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 93.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGG-PGVSDAYYCKECT
          ..FC.KQAGVAIGRLCE.CD.K.VICD..V.PCTLV..CDECN.GSYQG.C.ICGG..GVSDAYYCKECT
Retrocopy ICFC-KQAGVAIGRLCENCDSKRVICDRCVCPCTLVCLCDECNNGSYQGHCEICGG>VGVSDAYYCKECT

Parental  IQEKDRDGCPKIVNLGSSKTDLFYE
          .QEKDRDGCPKIV.LGSS.TDLF.E
Retrocopy SQEKDRDGCPKIVSLGSSETDLFHE

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	3.03 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.89 RPM
SRP007412_cerebellum	0.00 RPM	4.52 RPM
SRP007412_heart	0.00 RPM	4.24 RPM
SRP007412_kidney	0.00 RPM	3.99 RPM
SRP007412_liver	0.04 RPM	4.83 RPM
SRP007412_testis	0.34 RPM	4.75 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1471 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1471 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1471 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015687	1 retrocopy	retro_amel_1674,
Canis familiaris	ENSCAFG00000001090	1 retrocopy	retro_cfam_369,
Callithrix jacchus	ENSCJAG00000004999	3 retrocopies	retro_cjac_1194, retro_cjac_1527, retro_cjac_906,
Echinops telfairi	ENSETEG00000010741	1 retrocopy	retro_etel_102,
Homo sapiens	ENSG00000100410	3 retrocopies	retro_hsap_2033, retro_hsap_2647, retro_hsap_2829,
Gorilla gorilla	ENSGGOG00000001104	2 retrocopies	retro_ggor_1848, retro_ggor_1965,
Latimeria chalumnae	ENSLACG00000012094	1 retrocopy	retro_lcha_25,
Microcebus murinus	ENSMICG00000013520	1 retrocopy	retro_mmur_758,
Macaca mulatta	ENSMMUG00000011354	3 retrocopies	retro_mmul_1390, retro_mmul_1471 , retro_mmul_1503,
Mustela putorius furo	ENSMPUG00000016398	2 retrocopies	retro_mputfur_359, retro_mputfur_439,
Mus musculus	ENSMUSG00000061360	3 retrocopies	retro_mmus_1070, retro_mmus_1071, retro_mmus_1155,
Oryctolagus cuniculus	ENSOCUG00000012705	1 retrocopy	retro_ocun_640,
Otolemur garnettii	ENSOGAG00000002839	1 retrocopy	retro_ogar_55,
Pongo abelii	ENSPPYG00000011870	2 retrocopies	retro_pabe_1661, retro_pabe_2324,
Pan troglodytes	ENSPTRG00000014427	3 retrocopies	retro_ptro_1352, retro_ptro_1917, retro_ptro_2479,
Pteropus vampyrus	ENSPVAG00000001162	1 retrocopy	retro_pvam_66,
Rattus norvegicus	ENSRNOG00000024170	3 retrocopies	retro_rnor_2660, retro_rnor_2704, retro_rnor_2712,
Tarsius syrichta	ENSTSYG00000001082	1 retrocopy	retro_tsyr_259,
Tursiops truncatus	ENSTTRG00000003369	1 retrocopy	retro_ttru_1483,