RetrogeneDB ID: retro_mmul_2556

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:23035249..23035971(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL1
• Ensembl ID: ENSMMUG00000022148
• Aliases: None
• Description: methyltransferase like 1 [Source:HGNC Symbol;Acc:7030]

Sequence

>retro_mmul_2556
ATGGCAGCCAAGACTTGGAATGTGGCCAGAGCAGAGGCCCCGCAGCCCCAGAAGCACTACTACAGGTAACGTGCTGGCTC
CAACCCCATGGCAGACCACACACTGCGCTATCCTGTGAAGCCAGAGGAGATGGACTTGTCTGAGCTATACCCAGAGTTCT
TCGCTCCACTCACTCAAAATCAGAGCCACGATGACCCAAAGGGTAAGAGAGAAAAGAGAGCTCAGGCCCAAGCAGAGTTT
GCAGACACAGGCTGTGGCTATGGTGGCCTGTTAGTGGAACTATCACCGCTGTTCCCAGACACACTGATTCTGGGTCTGGA
GATCTGGGTGAAGGTCTCAGACTATGTACAAGACTGGATTCAGGCCCTACGTGCAGCTCCTGGAGGTGGCTTCCAGAACA
TTGCCTATCTCTGTAGCAATGCCATGAAGCACCTTCCTAACTTCTACAAGGGCCAGCTGACAAAGATGTTCTTCCTCTTC
CCCAACCCACATTTCAAGCAGACAAAGCACAAGTGGCAAATTATCAGTCCCACCCTGCTAGCAAAATGTGCCTATGTGCT
GAGAGTTGGGGGACTGGTATATACCATAACCTATGTGCTGGAGCTACACGACTGGATGTGCACTCATTTTGAAGAGCATC
TGCTGTTTGAGCATGTACCTCTGAGGACCTGAGTTAAGACCCCATTGTGGGACATCTAGGTACCTCAACTGAAGAGGGGA
AG

Alignment

ORF - retro_mmul_2556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 87.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAETWNVAGAEAPPPQKRYYRQRAHSNPMADHTLRYPVKPEEMDWSELYPEFFAPLTQNQSHDDPKDKK
          MAA.TWNVA.AEAP.PQK.YYR.RA.SNPMADHTLRYPVKPEEMD.SELYPEFFAPLTQNQSHDDPK.K.
Retrocopy MAAKTWNVARAEAPQPQKHYYR*RAGSNPMADHTLRYPVKPEEMDLSELYPEFFAPLTQNQSHDDPKGKR

Parental  EKRAQAQVEFADIGCGYGGLLVELSPLFPDTLILGLEIRVKVSDYVQDRIRALRAAPGGGFQNIACLRSN
          EKRAQAQ.EFAD.GCGYGGLLVELSPLFPDTLILGLEI.VKVSDYVQD.I.ALRAAPGGGFQNIA.L.SN
Retrocopy EKRAQAQAEFADTGCGYGGLLVELSPLFPDTLILGLEIWVKVSDYVQDWIQALRAAPGGGFQNIAYLCSN

Parental  AMKHLPNFFYKGQLTKMFFLFPDPHFKRTKHKWRIISPTLLAEYAYVLRVGGLVYTITDVLELHDWMCTH
          AMKHLPN.FYKGQLTKMFFLFP.PHFK.TKHKW.IISPTLLA..AYVLRVGGLVYTIT.VLELHDWMCTH
Retrocopy AMKHLPN-FYKGQLTKMFFLFPNPHFKQTKHKWQIISPTLLAKCAYVLRVGGLVYTITYVLELHDWMCTH

Parental  FEEHPLFERVPL-EDLSEDPIVGHLGTSTEEGK
          FEEH.LFE.VPL.EDLS.DPIVGHLGTSTEEGK
Retrocopy FEEHLLFEHVPL<EDLS*DPIVGHLGTSTEEGK

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	2.24 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.14 RPM
SRP007412_cerebellum	0.00 RPM	1.42 RPM
SRP007412_heart	0.00 RPM	3.65 RPM
SRP007412_kidney	0.00 RPM	15.96 RPM
SRP007412_liver	0.00 RPM	10.05 RPM
SRP007412_testis	0.00 RPM	7.01 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2556 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2556 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2556 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4796
Gorilla gorilla	retro_ggor_2985
Pongo abelii	retro_pabe_3730

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006615	1 retrocopy	retro_cjac_2888,
Homo sapiens	ENSG00000037897	1 retrocopy	retro_hsap_4796,
Gorilla gorilla	ENSGGOG00000001411	1 retrocopy	retro_ggor_2985,
Microcebus murinus	ENSMICG00000003803	1 retrocopy	retro_mmur_345,
Macaca mulatta	ENSMMUG00000022148	1 retrocopy	retro_mmul_2556 ,
Nomascus leucogenys	ENSNLEG00000017183	1 retrocopy	retro_nleu_1110,
Pongo abelii	ENSPPYG00000004706	1 retrocopy	retro_pabe_3730,
Tupaia belangeri	ENSTBEG00000011522	1 retrocopy	retro_tbel_3245,