RetrogeneDB ID: retro_mmul_2643

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:136475208..136475667(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000002687
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.12674
• Ensembl ID: ENSMMUG00000023659
• Aliases: None
• Description: MLN64 N-terminal domain homolog [Source:RefSeq peptide;Acc:NP_001253097]

Sequence

>retro_mmul_2643
ATGAACCATCTGGCAGAAGACATGGAGAACGCTCTCACCGGGAACCAGAACTCCCATGCTTCTCTGCGCAACGTCCATTC
TATCAACCCCACACAACTAATGGCCAGGATTGAGTCCTATGAAGGAAGGGAAAAGAAAGGCATATCTGATGTCAGGAGGA
CTTTCTGTTTGTGTGTCACCTTTGACCTCTTATTTGTAACGTTACTGTGGATAATAGAGTTAAATGTGAATGGAGGCATT
GAGAACACATTAGAGAAGGAGGTGATGCAGTATGACTACTATTCTTCGTATTTTGATATATTTCTTTTGGCAGTTTTTCG
ATTTAAAGGGTTAATACTTGCATGTGCTGTGTGCAGATTGCGCCATTGGTGGGCAATAGCGTTGACAACGGCAGTGACCA
GTGCCTTTTTACTAGCAAACGTGATCCTTTCAAAGCTTTTCTCTCAAGGGGCTTTTGGC

Alignment

ORF - retro_mmul_2643 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.77 %
• Parental protein coverage: 65.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNHLPEDMENALTGSQSSHASLRNIHSINPTQLMARIESYEGREKKGISDVRRTFCLFVTFDLLFVTLLW
          MNHL.EDMENALTG.Q.SHASLRN.HSINPTQLMARIESYEGREKKGISDVRRTFCL.VTFDLLFVTLLW
Retrocopy MNHLAEDMENALTGNQNSHASLRNVHSINPTQLMARIESYEGREKKGISDVRRTFCLCVTFDLLFVTLLW

Parental  IIELNVNGGIENTLEKEVMQYDYYSSYFDIFLLAVFRFKVLILAYAVCRLRHWWAIALTTAVTSAFLLAK
          IIELNVNGGIENTLEKEVMQYDYYSSYFDIFLLAVFRFK.LILA.AVCRLRHWWAIALTTAVTSAFLLA.
Retrocopy IIELNVNGGIENTLEKEVMQYDYYSSYFDIFLLAVFRFKGLILACAVCRLRHWWAIALTTAVTSAFLLAN

Parental  VILSKLFSQGAFG
          VILSKLFSQGAFG
Retrocopy VILSKLFSQGAFG

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	18.82 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	21.58 RPM
SRP007412_cerebellum	0.06 RPM	19.37 RPM
SRP007412_heart	0.00 RPM	11.60 RPM
SRP007412_kidney	0.00 RPM	16.43 RPM
SRP007412_liver	0.04 RPM	5.54 RPM
SRP007412_testis	0.04 RPM	8.97 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2643 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2643 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038795	1 retrocopy	retro_btau_264,
Choloepus hoffmanni	ENSCHOG00000008990	1 retrocopy	retro_chof_984,
Callithrix jacchus	ENSCJAG00000012622	1 retrocopy	retro_cjac_3042,
Cavia porcellus	ENSCPOG00000004394	1 retrocopy	retro_cpor_1237,
Dasypus novemcinctus	ENSDNOG00000017960	1 retrocopy	retro_dnov_2389,
Equus caballus	ENSECAG00000005250	1 retrocopy	retro_ecab_709,
Microcebus murinus	ENSMICG00000000945	1 retrocopy	retro_mmur_388,
Macaca mulatta	ENSMMUG00000023659	1 retrocopy	retro_mmul_2643 ,
Ictidomys tridecemlineatus	ENSSTOG00000014750	1 retrocopy	retro_itri_286,
Tursiops truncatus	ENSTTRG00000004099	1 retrocopy	retro_ttru_864,