RetrogeneDB ID: retro_mmul_1815

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:6230899..6231146(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MMU.1494
• Ensembl ID: ENSMMUG00000016841
• Aliases: None
• Description: snRNA-activating protein complex subunit 5 [Source:RefSeq peptide;Acc:NP_001248181]

Sequence

>retro_mmul_1815
CAGGAACTGCACAAGGAGGAGGAGACACTGCTCCCGTTGAAAGCAACCCTTGCACAACCTGGTGAATCACATCAAGGTTG
AAACATTGGCCCTCCAATCAACGATTAGTTCTAGGAGAGGGGATGAGGTGCTGTCTTCTCCAACATCTCCAACTGCGCCT
GAACAGTCACTTGTCATGTCAGTGCATATAGACAATGAAGCATCAGTCAACCAAACTACACTGGAGTGGAGCACAAAGAG
TCCTGTG

Alignment

ORF - retro_mmul_1815 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.08 %
• Parental protein coverage: 80.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QELRKEEETLLRLKAAL-HDQLNRLKVEELALQSMISSRRGDEMLSSHTVP---EQSHDMLVHVDNEASI
          QEL.KEEETLL.LKA.L.H...N..KVE.LALQS.ISSRRGDE.LSS.T.P...EQS..M.VH.DNEAS.
Retrocopy QELHKEEETLLPLKATL>HNLVNHIKVETLALQSTISSRRGDEVLSSPTSPTAPEQSLVMSVHIDNEASV

Parental  NQTTLELSTKSHV
          NQTTLE.STKS.V
Retrocopy NQTTLEWSTKSPV

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	0.11 RPM	15.91 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	13.33 RPM
SRP007412_cerebellum	0.00 RPM	16.79 RPM
SRP007412_heart	0.00 RPM	10.83 RPM
SRP007412_kidney	0.00 RPM	12.32 RPM
SRP007412_liver	0.00 RPM	6.85 RPM
SRP007412_testis	0.00 RPM	9.16 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1815 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1815 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1815 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2398

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017304	1 retrocopy	retro_cfam_1063,
Callithrix jacchus	ENSCJAG00000007484	1 retrocopy	retro_cjac_2314,
Dasypus novemcinctus	ENSDNOG00000006689	1 retrocopy	retro_dnov_1203,
Gorilla gorilla	ENSGGOG00000003693	1 retrocopy	retro_ggor_2398,
Macropus eugenii	ENSMEUG00000003990	1 retrocopy	retro_meug_1590,
Macaca mulatta	ENSMMUG00000016841	1 retrocopy	retro_mmul_1815 ,
Mus musculus	ENSMUSG00000032398	1 retrocopy	retro_mmus_702,
Nomascus leucogenys	ENSNLEG00000012935	1 retrocopy	retro_nleu_2325,
Oryctolagus cuniculus	ENSOCUG00000008791	1 retrocopy	retro_ocun_1059,
Rattus norvegicus	ENSRNOG00000010156	1 retrocopy	retro_rnor_1087,
Ictidomys tridecemlineatus	ENSSTOG00000009201	1 retrocopy	retro_itri_1582,
Tupaia belangeri	ENSTBEG00000014333	1 retrocopy	retro_tbel_68,