RetrogeneDB ID: retro_pabe_939

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:72197017..72198056(-)
• Located in intron of: ENSPPYG00000004776

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRS2
• Ensembl ID: ENSPPYG00000016278
• Aliases: None
• Description: magnesium transporter MRS2 homolog, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001127033]

Sequence

>retro_pabe_939
CAGAGAAATGTTACTTCTTTTGAAAGGAAGAAAACTGAGTTATACCAAGAGTTAGGTCTTCAAGCCAGAGATTTGAGATT
TCACTATGTAATGAGTATCACAGCCAGAAATCATAGGATTATCATGAGAATGGAGTATTTGAAAGCTGAGATAACTCCAG
AGTGTCTTCTGATATTAGATTATCATAATTTAAACTCACAGCAATGGCTGTTCTGGGAACTCTCTTCACAATTGTCTGGA
GAGGGTCAACTTGTTAGAAACCCTTTAATTTTTTGAGTTTAGAGCTATAGAAGCACTCCTGCAATACTGGATCAACACCC
TTCGGGGAAACTTAGCATTTTCCAACCACTGATCCTCGAGACGTTGGAAGCTTGGGTGGACCCCAAACATTCTTCCATAG
ACAGAAGCAAACTCCACATTTTACTACAGAATGGCAAAAGTCTATTAGAGTTAGAAACAGATAGTAAAATTTTCAGAGTC
AATTTTGGAGATCTTGGATGAGGAAGAGTTGCTAGAAGAGCTCTATCAAAATGGAGTGACCCACGAGTCTTTGAAAAGAG
CAGTATTGGGACTGACCATGCAGAGGAGATGGAGTTGCTGATGGAAAACTACTACCAACTAGTTGACGATGTCTCCAATG
CAGCTTAGGAGCTTCGGGTACTGACTGATGATTCACAAAGTATTACTTTCATCAATCTGGACAGCCACTGTAATGTGGTA
ATGAAGTCGAATCTACAGCTGACCATAAGAACCTTCTCTCTTTCGCTCTTTGGAGTAATGGGAGTTGCTTTTGGAATGAG
TTTGGAATCTTCCCTTGAAGAGGCCCATGGAGTGTTTTGACTGATTACAGGAATTATGTTCATGGGAACTGGCTCAGCTG
GAGGCACCTGCTTTCATTCCTTGGATGACAGCTAGAAGCTCCATTGCCTCCTAAGATGGCCTCCTTACCTAAAAAGATTC
TTCTGGCAGACAGAAGCGTGGAATGAAAAACAGCCTCAGACCTGATGCACTTGGATCAGGCAGGAGTATCCTAACAAAC

Alignment

ORF - retro_pabe_939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.56 %
• Parental protein coverage: 91.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  QGNVTSFERKKTELYQELGLQARDLRFQHVMSITVRNNRIIMRMEYLKAVITPECLLILDYRNLNLEQWL
          Q.NVTSFERKKTELYQELGLQARDLRF..VMSIT.RN.RIIMRMEYLKA.ITPECLLILDY.NLN..QWL
Retrocopy QRNVTSFERKKTELYQELGLQARDLRFHYVMSITARNHRIIMRMEYLKAEITPECLLILDYHNLNSQQWL

Parental  FRELPSQLSGEGQLVTYPLPF-EFRAIEALLQYWINTLQG-KLSVLQPLILETLDALVDPKHSSVDKSKL
          F.EL.SQLSGEGQLV..PL.F.EFRAIEALLQYWINTL.G.KLS..QPLILETL.A.VDPKHSS.D.SKL
Retrocopy FWELSSQLSGEGQLVRNPLIF>EFRAIEALLQYWINTLRG<KLSIFQPLILETLEAWVDPKHSSIDRSKL

Parental  HILLQNGKSLSELETD-IKIFKESILEILDEEELLEE-LCVSKWSDPQVFEKSSAGIDHAEEMELLLENY
          HILLQNGKSL.ELETD..K.F.ESILEILD.EE.L.E....SKWSDP.VFEKSS.G.DHAEEMELL.ENY
Retrocopy HILLQNGKSLLELETD>VK-FSESILEILD-EEELLE<RALSKWSDPRVFEKSSIGTDHAEEMELLMENY

Parental  YRLADDLSNAARELRVLIDDSQSIIFINLDSHRNVMMRLNLQLTMGTFSLSLFGLMGVAFGMNLESSLEE
          Y.L.DD.SNAA.ELRVL.DDSQSI.FINLDSH.NV.M..NLQLT..TFSLSLFG.MGVAFGM.LESSLEE
Retrocopy YQLVDDVSNAA*ELRVLTDDSQSITFINLDSHCNVVMKSNLQLTIRTFSLSLFGVMGVAFGMSLESSLEE

Parental  DHRIFWLITGIMFMGSG-LIWRRLLSFLGRQLEAPLPPMMASLPKKTLLADRSME-LKNSLRLDGLGSGR
          .H..F.LITGIMFMG.G.L.WR.LLSFLG.QLEAPLPP.MASLPKK.LLADRS.E..KNSLR.D.LGSGR
Retrocopy AHGVF*LITGIMFMGTG<LSWRHLLSFLG*QLEAPLPPKMASLPKKILLADRSVE<MKNSLRPDALGSGR

Parental  SILTN
          SILTN
Retrocopy SILTN

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_prefrontal_cortex	0.00 RPM	1.94 RPM
SRP007412_cerebellum	0.00 RPM	2.80 RPM
SRP007412_heart	0.00 RPM	2.74 RPM
SRP007412_kidney	0.03 RPM	1.79 RPM
SRP007412_liver	0.00 RPM	0.83 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_939 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_939 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_939 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_878

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006424	1 retrocopy	retro_dnov_1486,
Equus caballus	ENSECAG00000013105	1 retrocopy	retro_ecab_1032,
Homo sapiens	ENSG00000124532	1 retrocopy	retro_hsap_4006,
Gorilla gorilla	ENSGGOG00000009098	1 retrocopy	retro_ggor_2689,
Macaca mulatta	ENSMMUG00000001018	2 retrocopies	retro_mmul_2312, retro_mmul_878,
Pongo abelii	ENSPPYG00000016278	1 retrocopy	retro_pabe_939 ,
Pan troglodytes	ENSPTRG00000017774	1 retrocopy	retro_ptro_2720,