RetrogeneDB ID: retro_mmul_2029

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:99282488..99282931(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000007850
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.10922
• Ensembl ID: ENSMMUG00000028767
• Aliases: None
• Description: eukaryotic translation initiation factor 3 subunit K [Source:RefSeq peptide;Acc:NP_001244620]

Sequence

>retro_mmul_2029
ATGTTGATATTTGAGCAGATGAGAGCCAGTGTGGGCAAGCTGCTCAAGGGTATCAACAGGAACAATCCTGAGAAGCTGGC
CACCCTGGAGTGCTCTGTGGAGATGCAGGTCAAAGAGAATGCCTATGATCTGGAAGCCAACCCAGCTGTCCTGAAGCTGT
ACCAGTCCAACCCAGCATTTTTTCAGACCACGATCACTGCCCAGATCCAGCTGAAGGCCCTCACCAACCTGCCACATACC
AACTTCATGCTGTGCAAGTGCATGATTGGCCAGGCACATCAAGAAGAGTGGCCATCCGATGCATTTTGTACCTCAAGGAC
CTGGAGACCAGCCTCTTTCAGGCCTTCTGGCAAGCCTTAGATGAAAACATGGACCTCTTGGAAGGTATAACTGGCTTTGA
AGACTCTGTCTGAATGCTTATCTGCCCTGTCATGGGTATCACC

Alignment

ORF - retro_mmul_2029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.67 %
• Parental protein coverage: 68.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMFEQMRANVGKLLKGIDRYNPENLATLERYVETQAKENAYDLEANLAVLKLYQFNPAFFQTTVTAQIL
          M..FEQMRA.VGKLLKGI.R.NPE.LATLE..VE.Q.KENAYDLEAN.AVLKLYQ.NPAFFQTT.TAQI.
Retrocopy MLIFEQMRASVGKLLKGINRNNPEKLATLECSVEMQVKENAYDLEANPAVLKLYQSNPAFFQTTITAQIQ

Parental  LKALTNLPHTDFTLCKCMIDQAHQEERP-IRQILYLGDLLETCHFQAFWQALDENMDLLEGITGFEDSVR
          LKALTNLPHT.F.LCKCMI.QAHQEE.P.IR.ILYL.D.LET..FQAFWQALDENMDLLEGITGFEDSV.
Retrocopy LKALTNLPHTNFMLCKCMIGQAHQEEWP<IRCILYLKD-LETSLFQAFWQALDENMDLLEGITGFEDSV*

Parental  KFICHVVGIT
          ..IC.V.GIT
Retrocopy MLICPVMGIT

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	14.23 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	34.35 RPM
SRP007412_cerebellum	0.00 RPM	10.59 RPM
SRP007412_heart	0.00 RPM	28.62 RPM
SRP007412_kidney	0.00 RPM	15.02 RPM
SRP007412_liver	0.00 RPM	24.98 RPM
SRP007412_testis	0.00 RPM	18.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2029 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2029 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2029 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3224
Pan troglodytes	retro_ptro_2176
Gorilla gorilla	retro_ggor_2192
Pongo abelii	retro_pabe_2673
Macaca mulatta	retro_mmul_2098

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007594	3 retrocopies	retro_etel_1653, retro_etel_1868, retro_etel_5,
Homo sapiens	ENSG00000178982	2 retrocopies	retro_hsap_2616, retro_hsap_3224,
Gorilla gorilla	ENSGGOG00000016808	1 retrocopy	retro_ggor_2192,
Myotis lucifugus	ENSMLUG00000010217	1 retrocopy	retro_mluc_645,
Macaca mulatta	ENSMMUG00000028767	2 retrocopies	retro_mmul_1478, retro_mmul_2029 ,
Monodelphis domestica	ENSMODG00000013314	3 retrocopies	retro_mdom_1235, retro_mdom_1929, retro_mdom_781,
Otolemur garnettii	ENSOGAG00000026260	1 retrocopy	retro_ogar_413,
Pongo abelii	ENSPPYG00000025857	4 retrocopies	retro_pabe_2342, retro_pabe_2555, retro_pabe_2610, retro_pabe_2673,
Pan troglodytes	ENSPTRG00000010934	2 retrocopies	retro_ptro_1763, retro_ptro_2176,
Sarcophilus harrisii	ENSSHAG00000005313	1 retrocopy	retro_shar_689,
Tarsius syrichta	ENSTSYG00000007001	1 retrocopy	retro_tsyr_1964,