RetrogeneDB ID: retro_pabe_2804

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:179952253..179952957(-)
• Located in intron of: ENSPPYG00000016084

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRMT8
• Ensembl ID: ENSPPYG00000004159
• Aliases: None
• Description: protein arginine methyltransferase 8 [Source:HGNC Symbol;Acc:5188]

Sequence

>retro_pabe_2804
TTTGGCAACTCCATGTTTCACAACCGGCACCTCTTTAAAGACAAGGTGGTGCTGGATGTGGGCTCGGACACAAGCATCCT
CTGCATGTTCGCCGCCAAGGCCGGGCCCGCAAGGTCATCGGCATCGAGTGTTCCAGTAGCTCTGATTATGCGGTGAAGAT
TGTCAAAGCCAACAAGTTAAAACACTTGGTGACCATCACCAAGGGGAAGGTGGAGGAGGTAGAGCTCCCGGTGGAAAAGG
TGGACATCATCATCAGCAAGTGGATGGGCAAACTGCCTCTTCTACGAGTCCATGCTCAACACCGTGCTCTATGCCCGGAC
AAGTGGCTGGCGCCCAATAGCCTCATCTTCCCAGACCGGGCCACACTGTATGTGACGGCCACCGAGGACTGGCAGTACAA
AGACTACAAGATCCACTGGTGGGAGAACGTTTATGGCTTCGATATATCTTGCATCAAAGATGTGGCCATCAAGGAACCCC
TAGTGGATGTGGTGGACCTCAAACAGCTGGTCACCAACGCCTGCCTCATAAAGAAGGTAGACATCTACACCGTCAAGGTG
GAAGACCTGACCTTCACCTTCCCGTTCTGCCTGCAAGTGAAGCAGAATGACTACGTGCACGCCCACGTGGCCTACTTCAA
CATCGAGTTTACGCACTGCCACAAGAGGACCGGCTTCTCTCCACCATACCCAAGTCCCTGTACA

Alignment

ORF - retro_pabe_2804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.53 %
• Parental protein coverage: 59.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YRNSMYHNKHVFKDKVVLDVGSGTGILSMFAAKAG-AKKVFGIECSSISDYSEKIIKANHLDSIITIFKG
          ..NSM.HN.H.FKDKVVLDVGS.T.IL.MFAAKAG.A.KV.GIECSS.SDY..KI.KAN.L....TI.KG
Retrocopy FGNSMFHNRHLFKDKVVLDVGSDTSILCMFAAKAG<ARKVIGIECSSSSDYAVKIVKANKLKHLVTITKG

Parental  KVEEVELPVEKVDIIISEWMG-YCLFYESMLNTVIFAR-DKWLKPGGLMFPDRAALYVVAIEDRQYKDFK
          KVEEVELPVEKVDIIIS.WMG..CLFYESMLNTV..AR.DKWL.P..L.FPDRA.LYV.A.ED.QYKD.K
Retrocopy KVEEVELPVEKVDIIISKWMG>NCLFYESMLNTVLYAR<DKWLAPNSLIFPDRATLYVTATEDWQYKDYK

Parental  IHWWENVYGFDMTCIRDVAMKEPLVDIVDPKQVVTNACLIKEVDIYTVKTEELSFTSAFCLQIQRNDYVH
          IHWWENVYGFD..CI.DVA.KEPLVD.VD.KQ.VTNACLIK.VDIYTVK.E.L.FT..FCLQ...NDYVH
Retrocopy IHWWENVYGFDISCIKDVAIKEPLVDVVDLKQLVTNACLIKKVDIYTVKVEDLTFTFPFCLQVKQNDYVH

Parental  ALVTYFNIEFTKCHKKMGFSTAPDAPYT
          A.V.YFNIEFT.CHK..GFS.....P.T
Retrocopy AHVAYFNIEFTHCHKRTGFSPPYPSPCT

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	9.29 RPM	29.30 RPM
SRP007412_cerebellum	7.42 RPM	9.73 RPM
SRP007412_heart	4.91 RPM	0.00 RPM
SRP007412_kidney	5.83 RPM	0.00 RPM
SRP007412_liver	2.78 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2804 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2804 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2804 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3406
Pan troglodytes	retro_ptro_2313
Gorilla gorilla	retro_ggor_2305
Macaca mulatta	retro_mmul_2121
Callithrix jacchus	retro_cjac_1800

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000004075	1 retrocopy	retro_meug_455,
Nomascus leucogenys	ENSNLEG00000002986	1 retrocopy	retro_nleu_2941,
Pongo abelii	ENSPPYG00000004159	1 retrocopy	retro_pabe_2804 ,
Pan troglodytes	ENSPTRG00000004543	1 retrocopy	retro_ptro_2313,
Tupaia belangeri	ENSTBEG00000000940	1 retrocopy	retro_tbel_750,