RetrogeneDB ID: retro_mmul_2251

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:113339743..113340378(-)
• Located in intron of: ENSMMUG00000007468

Retrocopy information

• Ensembl ID: ENSMMUG00000029361
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.4582
• Ensembl ID: ENSMMUG00000016239
• Aliases: None
• Description: None

Sequence

>retro_mmul_2251
ATGGCGACCGCGGCGCGTGTTGTGGGCCGGCTGCCCGCGCTGTGTAGCGGGACGGCAGGTCATTTATTGGGGAGGCAGCG
TTCCCTAAGCACCTTACCAGCAGCTTCCATTTTGGTGTGGAAGAGTGCTCTGAGCAATGGCTGTTTGTCATCACTGGGAA
CCAGAGACACCCATCCCTACGCCAGCTTGAGCCACGCGCTGCAGACACAATGCTGTGTTTCTTCTCCCAGTCACCTGATG
GGCCAGCAATATAGACCATATAGTTTCTTCACTAAATTGACTGCAGATGAGCTGTGGAAAGGCGCTTTAGCGGAGAGTGG
TGCCGGATCAAGAAAAGGAAGAGGCAAAAGAACTAAAAAGAGGAAAAGAAAGGATCTGAACAGGGGTCAGATCATTGGGA
AGGGCATTACGGTTTTCTGTGGCCTGGTCTGAATGTCCCTCTTATGAAAAATGGAGCAGTGCAGACCATCGCCCAAAGAA
GCAAGGAAGAGCAGAAGAAGATGGAGGCCGACATGATCCAGCAGAGAGAAGAGTGGGACCGAAAGAGGAAGATAAAGGTT
AAACGCGAGCGAGGATGGAGTGGAAACTCCTGGGGAGGCGTCAGTCTTGGCCCCCCTGACCCTGGCCCCAATGGA

Alignment

ORF - retro_mmul_2251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.18 %
• Parental protein coverage: 59.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATAARVVGRLPALCSGTAGHLLGRQRSLSTLPAASILAWKSALSNGCLSSLGTRDTHPYASLSHALQTQ
          MATAARVVGRLPALCSGTAGHLLGRQRSLSTLPAASIL.WKSALSNGCLSSLGTRDTHPYASLSHALQTQ
Retrocopy MATAARVVGRLPALCSGTAGHLLGRQRSLSTLPAASILVWKSALSNGCLSSLGTRDTHPYASLSHALQTQ

Parental  CCVSSPSHLMGQQYRPYSFFTKLTADELWKGALAESGAGSRKGRGKRTKKRKRKDLNRGQIIG-EGHYGF
          CCVSSPSHLMGQQYRPYSFFTKLTADELWKGALAESGAGSRKGRGKRTKKRKRKDLNRGQIIG.EGHYGF
Retrocopy CCVSSPSHLMGQQYRPYSFFTKLTADELWKGALAESGAGSRKGRGKRTKKRKRKDLNRGQIIG<EGHYGF

Parental  LWPGLNVPLMKNGAVQTIAQRSKEEQKKMEADMIQQREEWYRKRKIKVKHERGWTGNSWGGVSLGPPGPG
          LWPGLNVPLMKNGAVQTIAQRSKEEQKKMEADMIQQREEW.RKRKIKVK.ERGW.GNSWGGVSLGPP.PG
Retrocopy LWPGLNVPLMKNGAVQTIAQRSKEEQKKMEADMIQQREEWDRKRKIKVKRERGWSGNSWGGVSLGPPDPG

Parental  PNG
          PNG
Retrocopy PNG

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	18.04 RPM
SRP007412_brain_prefrontal_cortex	0.40 RPM	27.21 RPM
SRP007412_cerebellum	0.06 RPM	12.53 RPM
SRP007412_heart	0.24 RPM	37.27 RPM
SRP007412_kidney	0.12 RPM	21.13 RPM
SRP007412_liver	0.04 RPM	13.02 RPM
SRP007412_testis	0.15 RPM	26.42 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2251 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2251 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2251 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009757	1 retrocopy	retro_amel_1242,
Callithrix jacchus	ENSCJAG00000018942	1 retrocopy	retro_cjac_2129,
Homo sapiens	ENSG00000144029	1 retrocopy	retro_hsap_3116,
Gorilla gorilla	ENSGGOG00000001750	1 retrocopy	retro_ggor_2139,
Microcebus murinus	ENSMICG00000007318	1 retrocopy	retro_mmur_565,
Myotis lucifugus	ENSMLUG00000003183	1 retrocopy	retro_mluc_2245,
Macaca mulatta	ENSMMUG00000016239	2 retrocopies	retro_mmul_2110, retro_mmul_2251 ,
Mus musculus	ENSMUSG00000027374	1 retrocopy	retro_mmus_2014,
Nomascus leucogenys	ENSNLEG00000000002	1 retrocopy	retro_nleu_1438,
Pongo abelii	ENSPPYG00000012051	1 retrocopy	retro_pabe_2574,
Pan troglodytes	ENSPTRG00000012209	1 retrocopy	retro_ptro_2107,