RetrogeneDB ID: retro_mmul_2024

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:89742445..89743462(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000020362
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RG9MTD2
• Ensembl ID: ENSMMUG00000009090
• Aliases: None
• Description: None

Sequence

>retro_mmul_2024
ATGTCATCTGAAATGTTGCCAGCATTTTGTGAAACTTCTAATGTTGACAAAAAGCAAGGCATAAATGAACATCAAAAAGA
AAGCCAGAAGCCAAGATTAGGTAAAGGGTGTGAACCAGTATCTAAACGACAAATGAAAAAACTAATAAAACAGAAACAAC
GGGAAGAGCAATGGGAACTCCGCAAACAAAAGCGGAAAGAAAAACACTAGAGGAAAAAATTGGAGCGACAATGTCAAATG
GAATCAAACTCAGATGGAAATGACAGAAAACATGTTCGAAGAGATGTTGTTCATAGCACCCTTCACCTCATTATTGACTG
TAGTTTTGATGACTTGATGGTATTAAAGGACATTAAGAAACTTCATAAGCAGATTCAACGATGTTATGCAGAAAACCGAC
GGGCACTGCATCCTGTGCAGTTTTACTTGACAAGCCATGGAGGTCAGCTGAACAACAACATGGATGAAAATGACAAAGGA
TGGGTCAACTGGAAGGATATCCATATCAAACCAGAGCACTATAGTGAACTCATAAAAAAAAGAAGACCTGATTTATCTTA
CATCAGATTCACCTAATATACTGAAGGAATTAGATGAATCAAAGGCTTATGTGATTGGAGGATTAGTAGATCACAACCAT
CACAAGGGACTCACATATAAACAAGCATCAGATTATGGAATCAATCATGCACAGCTCCTGCTTGGAAATTTTGTGAAGAT
GAATAGTCGAAAAGTTTTGGCAGTTAATCATGTGTTTGAGATTATTCTGGAATACCTGGAAACAAGAGACTGGCAAGAAG
CATTTTTTACTATCTTCCCCAATGGAAAGGAGCTGTTCCCACAGACAAAACCTGTGAAAGTGCTTCTTATGACAATCAGT
CTGTCAGGATGGAGGAATGTGGATCGGACAGTGATTCCAGTGAGACGGAAGATAGCAGAAATGAACTAGATTCACCACGT
GAAGAAAAGCAGGATAAGGAAAATCACGCTGAATCTACAGTGAACTCTCTGCCACAC

Alignment

ORF - retro_mmul_2024 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.96 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSEMLPAFIETSNVDKKQGINEHQEESQKPRLGEGCEPISKRQMKKLIKQKQWEEQRELRKQKRKEKRK
          MSSEMLPAF.ETSNVDKKQGINEHQ.ESQKPRLG.GCEP.SKRQMKKLIKQKQ.EEQ.ELRKQKRKEK..
Retrocopy MSSEMLPAFCETSNVDKKQGINEHQKESQKPRLGKGCEPVSKRQMKKLIKQKQREEQWELRKQKRKEKH*

Parental  RKKLERQCQMESNSDGNDRKRVRRDVVHSTLRLIIDCSFDDLMVLKDIKKLHKQIQRCYAENRRALHPVQ
          RKKLERQCQMESNSDGNDRK.VRRDVVHSTL.LIIDCSFDDLMVLKDIKKLHKQIQRCYAENRRALHPVQ
Retrocopy RKKLERQCQMESNSDGNDRKHVRRDVVHSTLHLIIDCSFDDLMVLKDIKKLHKQIQRCYAENRRALHPVQ

Parental  FYLTSHGGQLKKNMDENDKGWVNWKDIHIKPEHYSEL-IKKEDLIYLTSDSPNILKELDESKAYVIGGLV
          FYLTSHGGQL..NMDENDKGWVNWKDIHIKPEHYSEL....EDLIYLTSDSPNILKELDESKAYVIGGLV
Retrocopy FYLTSHGGQLNNNMDENDKGWVNWKDIHIKPEHYSEL>XXXEDLIYLTSDSPNILKELDESKAYVIGGLV

Parental  DHNHHKGLTYKQASDYGINHAQLPLGNFVKMNSRKVLAVNHVFEIILEYLETRDWQEAFFTI-LPQRKGA
          DHNHHKGLTYKQASDYGINHAQL.LGNFVKMNSRKVLAVNHVFEIILEYLETRDWQEAFFTI.LPQ.KGA
Retrocopy DHNHHKGLTYKQASDYGINHAQLLLGNFVKMNSRKVLAVNHVFEIILEYLETRDWQEAFFTI<LPQWKGA

Parental  VPTDKTCESASYDPQSVRMEECGSDSDSSEEEDSRNELDSPREEKQDKENHTESIGNSLPH
          VPTDKTCESASYD.QSVRMEECGSDSDSSE.EDSRNELDSPREEKQDKENH.ES..NSLPH
Retrocopy VPTDKTCESASYDNQSVRMEECGSDSDSSETEDSRNELDSPREEKQDKENHAESTVNSLPH

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	3.25 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.98 RPM
SRP007412_cerebellum	0.00 RPM	1.36 RPM
SRP007412_heart	0.00 RPM	1.12 RPM
SRP007412_kidney	0.00 RPM	2.58 RPM
SRP007412_liver	0.00 RPM	1.07 RPM
SRP007412_testis	0.08 RPM	6.67 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2024 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2024 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2024 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000009090	1 retrocopy	retro_mmul_2024 ,
Mus musculus	ENSMUSG00000004127	3 retrocopies	retro_mmus_3007, retro_mmus_3008, retro_mmus_3368,
Oryctolagus cuniculus	ENSOCUG00000015213	1 retrocopy	retro_ocun_1482,
Otolemur garnettii	ENSOGAG00000005330	2 retrocopies	retro_ogar_2061, retro_ogar_3335,