RetrogeneDB ID: retro_mmul_2022

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:87714085..87714646(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000007275
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.4793
• Ensembl ID: ENSMMUG00000014761
• Aliases: RAB5C, RAB5L
• Description: ras-related protein Rab-5C [Source:RefSeq peptide;Acc:NP_001253100]

Sequence

>retro_mmul_2022
TCTGCAGTGGGCAAATCCAACCTGTCCTCTGCCTTGTGAAGGGACAATTTCATGAGTACCAGGAGAGCACAATCGGAGCA
GCCTTCCTCACACAGAATGTCTGCTTGGACAACACAACAGTCAGGTTTGAGATCTGGGACATGGTTGGACAGGAGTGGTA
TCACAGCCTGGCCGCCATGTATTCTTGGGAAGCCCAGGCTGCCATCATGGTCTATGACGTCACCAATACAGATACATTTG
CTGGAGATAAGAACTGGGTGAAGGAGCTATCGAGGCAGGCCAGCCCCAACATGGTCCTTGCACTCACAGGTAACAAGGCA
GACCTGGCCAGTAAGAAAGCCCTGGAATTCCAGGAAGCACAAGCCTATACAGACAACAACAGTTGGCTGTTCATGGAGAC
ATCAGCAAAGGCTGCAATGAATGTGAATGAAATTTTCATGGCAATAGCTGAGAAGCTTCCCAAGAACAAGCCCCAGAATG
CAGCTGGTGCTCCAGACAGAAACCAAGGTGTGGGACCTCCAGGAGAACCAGCCGGCCAGCCCCAGCCAGTGTTGCAGCAA
T

Alignment

ORF - retro_mmul_2022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.95 %
• Parental protein coverage: 86.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SAVGKSSL-VLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAI
          SAVGKS.L.VL..VKGQFHEYQESTIGAAFLTQ.VCLD.TTV.FEIWD..GQE.YHSLA.MY...AQAAI
Retrocopy SAVGKSNL<VLCLVKGQFHEYQESTIGAAFLTQNVCLDNTTVRFEIWDMVGQEWYHSLAAMYSWEAQAAI

Parental  VVYDITNTDTFARAKNWVKELQRQASPNIVIALAGNKADLASKRAVEFQEAQAYADDNSLLFMETSAKTA
          .VYD.TNTDTFA..KNWVKEL.RQASPN.V.AL.GNKADLASK.A.EFQEAQAY.D.NS.LFMETSAK.A
Retrocopy MVYDVTNTDTFAGDKNWVKELSRQASPNMVLALTGNKADLASKKALEFQEAQAYTDNNSWLFMETSAKAA

Parental  MNVNEIFMAIAKKLPKNEPQNATGAPGRNRGV-DLQENNPASRSQCCSN
          MNVNEIFMAIA.KLPKN.PQNA.GAP.RN.GV.DLQEN.PAS.SQCCSN
Retrocopy MNVNEIFMAIAEKLPKNKPQNAAGAPDRNQGV>DLQENQPASPSQCCSN

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	47.96 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	108.84 RPM
SRP007412_cerebellum	0.00 RPM	40.10 RPM
SRP007412_heart	0.00 RPM	32.80 RPM
SRP007412_kidney	0.00 RPM	101.76 RPM
SRP007412_liver	0.00 RPM	80.00 RPM
SRP007412_testis	0.00 RPM	43.69 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2022 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2022 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2022 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3216
Pan troglodytes	retro_ptro_2237
Pongo abelii	retro_pabe_2664

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Gorilla gorilla	ENSGGOG00000005472	1 retrocopy	retro_ggor_2182,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118,
Macaca mulatta	ENSMMUG00000005692	1 retrocopy	retro_mmul_1557,
Macaca mulatta	ENSMMUG00000006992	2 retrocopies	retro_mmul_227, retro_mmul_839,
Macaca mulatta	ENSMMUG00000014761	1 retrocopy	retro_mmul_2022 ,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,
Pan troglodytes	ENSPTRG00000009194	1 retrocopy	retro_ptro_2237,
Tupaia belangeri	ENSTBEG00000007092	1 retrocopy	retro_tbel_4668,