RetrogeneDB ID: retro_mmul_1764

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:51907567..51908221(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A20
• Ensembl ID: ENSMMUG00000015418
• Aliases: None
• Description: solute carrier family 25 (carnitine/acylcarnitine translocase), member 20 [Source:RefSeq peptide;Acc:NP_001252793]

Sequence

>retro_mmul_1764
ATGGCTGATCAGCCGAAGCCCATCAGCCCGCTCAAGAACCTGCTGGCCAGCGGCTTTGGTGGCATGTGCCTGCTGTTCAT
GGGGCACCCTCTGGACACCGTCAAGGTCCGACTGCAGACACAGCTACCGAGTTTGCCTAGACAGCCTCCCATGTACTCTG
GGACCTTGGACTGTCTCCCGAAGACTCTTAGAAGGGGCATCACGGGGCTATATCAGTGAATGGCTGCTCCTATCATCGGT
GTCACCCCCATGTTTGCTGTGTACTTCTTTGGGTTTGGTTAAAGGAAGAAACTACGACAGAAACACCCAGAGGATGTGCT
CAGCTATCCCCAGCTGTTTGCAGCTGGTATGTTATCTGGTACATTCACCACAGGCATCGTGACCCCTGGAGCACCCATCA
AGTGCTGGTTACAGTTTCAGGCTTCTTCAGGGGAAACCAAGTACATTGGAACCTTGGACTGTGCAAAGAAGCTGTACCAG
GAGTTTGGGATCCGAGGCATCTACAAAGGGACCGTGCTTACCCTTATGTGAGATGTTCCAGCTAGTGGAATGTAATTCAT
AACATATAAATGGCTAAAAAATATCTTCACTCCTGAAGGAAAGAGGGTCCGTGAGCTCAGTGCGCCTTGAATCCTGGCGG
CTGGGGGCATTGCC

Alignment

ORF - retro_mmul_1764 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.93 %
• Parental protein coverage: 72.76 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADQPKPISPLKNLLAGGFGGVCLVFVGHPLDTVKVRLQTQPPSLPGQPPMYSGTFDCFRKTLFREGIRG
          MADQPKPISPLKNLLA.GFGG.CL.F.GHPLDTVKVRLQTQ.PSLP.QPPMYSGT.DC..KTL.R.GI.G
Retrocopy MADQPKPISPLKNLLASGFGGMCLLFMGHPLDTVKVRLQTQLPSLPRQPPMYSGTLDCLPKTL-RRGITG

Parental  LYRGMAAPIIGVTPMFAVCFFGFGLGKKLQQKHPEDVLSYPQLFAAGMLSGVFTTGIMTPGERIKCLLQI
          LY..MAAPIIGVTPMFAV.FFGFG..KKL.QKHPEDVLSYPQLFAAGMLSG.FTTGI.TPG..IKC.LQ.
Retrocopy LYQ*MAAPIIGVTPMFAVYFFGFG*RKKLRQKHPEDVLSYPQLFAAGMLSGTFTTGIVTPGAPIKCWLQF

Parental  QASSGETKYTGTLDCAKKLYQEFGIRGIYKGTVLTLMRDVPASGMYFMTYEWLKNIFTPEGKRVSELSVP
          QASSGETKY.GTLDCAKKLYQEFGIRGIYKGTVLTLM.DVPASGM.F.TY.WLKNIFTPEGKRV.ELS.P
Retrocopy QASSGETKYIGTLDCAKKLYQEFGIRGIYKGTVLTLM*DVPASGM*FITYKWLKNIFTPEGKRVRELSAP

Parental  RILVAGGIA
          .IL.AGGIA
Retrocopy *ILAAGGIA

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	6.27 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	7.14 RPM
SRP007412_cerebellum	0.00 RPM	7.10 RPM
SRP007412_heart	0.06 RPM	13.19 RPM
SRP007412_kidney	0.00 RPM	24.65 RPM
SRP007412_liver	0.04 RPM	70.14 RPM
SRP007412_testis	0.08 RPM	6.29 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1764 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1764 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1764 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3469
Pan troglodytes	retro_ptro_2352
Gorilla gorilla	retro_ggor_2341
Pongo abelii	retro_pabe_2865
Callithrix jacchus	retro_cjac_2338

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003285	1 retrocopy	retro_cjac_2338,
Homo sapiens	ENSG00000178537	1 retrocopy	retro_hsap_3469,
Gorilla gorilla	ENSGGOG00000028046	1 retrocopy	retro_ggor_2341,
Macaca mulatta	ENSMMUG00000015418	1 retrocopy	retro_mmul_1764 ,
Monodelphis domestica	ENSMODG00000013383	3 retrocopies	retro_mdom_1584, retro_mdom_229, retro_mdom_266,
Nomascus leucogenys	ENSNLEG00000006700	1 retrocopy	retro_nleu_342,
Pongo abelii	ENSPPYG00000013892	1 retrocopy	retro_pabe_2865,
Pan troglodytes	ENSPTRG00000014900	1 retrocopy	retro_ptro_2352,
Drosophila melanogaster	FBgn0031881	1 retrocopy	retro_dmel_15,