RetrogeneDB ID: retro_ptro_2313

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:178340246..178341136(-)
• Located in intron of: ENSPTRG00000017575

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRMT8
• Ensembl ID: ENSPTRG00000004543
• Aliases: None
• Description: protein arginine methyltransferase 8 [Source:HGNC Symbol;Acc:5188]

Sequence

>retro_ptro_2313
TTCGGCAACTCCATGTTTCACAACCGGCACCTCTTTAAAGACAAGGTGGTGCTGGATGTGGGCTCGGATACAAGCATCCT
CTGCATGTTCGCCGCCAAGGCCGGGCCCGCAAGGTCATCGGCATCGAGTGTTCCAGTAGCTCTGATTATGCGGTGAAGAT
TGTCGAAGCCAACAAGTTAGACCACTTGGTGACCATCACCAAGGGGAAGGTGGAGGAGATAGAGCTCCCGGTGGAAAAGG
TGAACATCATCATCAGCAAGTGGATGGGCTAACTGCCTCTTCTACGAGTCCATGCTCAACACTGTGCTCTATGCCCGGAC
AAGTGGCTGGCGCCCAATAGCCTCACCTTCCCAGACCGGGCCACACTGTATGTGACGGCCACCGACGACCGGCAGTACAA
AGACTACAAGATCCACTGGTGGGAGAACGTTTATGGCTTCGATATATCTTGCATCAAAGATGTGGCCGTCAAGGAAACCC
TAGTGGATGTGGTGGACCTCAAACAGCTGGTTACCAACGCCTGCCTCATAAAGGAGGTAGACATCTACACCGTCAAGGTG
GAAGACCTGACCTTCACCTCCCCGTTCTGCCTGCAAGTGAAGCAGAATGACTACGTGCACACCCAGGTGGCCTACTTCAA
CATCGAGTTTATGCACTGCCACAAGAGGACCGGAGGGACCGGCTTCTCCACCATACCCGAGTCCCTGTACACGCACTGGA
AGCAGACGGTGTTCTACATGGAGGACTACCTGACCTTGAAGACAGGCGAGGAGATCTTCGGCACCATCGGCATGCGGCCC
AACGCCAAGAACTGGGACCGGGACTTCACCATCAACCTAGATTTCAGGGGCCATCTGTGCGACCTGTCCTGCTCCACAGA
CTACAGGATG

Alignment

ORF - retro_ptro_2313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 76.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YRNSMYHNKHVFKDKVVLDVGSGTGILSMFAAKAG-AKKVFGIECSSISDYSEKIIKANHLDNIITIFKG
          ..NSM.HN.H.FKDKVVLDVGS.T.IL.MFAAKAG.A.KV.GIECSS.SDY..KI..AN.LD...TI.KG
Retrocopy FGNSMFHNRHLFKDKVVLDVGSDTSILCMFAAKAG<ARKVIGIECSSSSDYAVKIVEANKLDHLVTITKG

Parental  KVEEVELPVEKVDIIISEWMG-YCLFYESMLNTVIFAR-DKWLKPGGLMFPDRAALYVVAIEDRQYKDFK
          KVEE.ELPVEKV.IIIS.WMG..CLFYESMLNTV..AR.DKWL.P..L.FPDRA.LYV.A..DRQYKD.K
Retrocopy KVEEIELPVEKVNIIISKWMG>NCLFYESMLNTVLYAR<DKWLAPNSLTFPDRATLYVTATDDRQYKDYK

Parental  IHWWENVYGFDMTCIRDVAMKEPLVDIVDPKQVVTNACLIKEVDIYTVKTEELSFTSAFCLQIQRNDYVH
          IHWWENVYGFD..CI.DVA.KE.LVD.VD.KQ.VTNACLIKEVDIYTVK.E.L.FTS.FCLQ...NDYVH
Retrocopy IHWWENVYGFDISCIKDVAVKETLVDVVDLKQLVTNACLIKEVDIYTVKVEDLTFTSPFCLQVKQNDYVH

Parental  ALVTYFNIEFTKCHKKMG---FSTAPDAPYTHWKQTVFYLEDYLTVRRGEEIYGTISMKPNAKNVRDLDF
          ..V.YFNIEF..CHK..G...FST.P...YTHWKQTVFY.EDYLT...GEEI.GTI.M.PNAKN..D.DF
Retrocopy TQVAYFNIEFMHCHKRTGGTGFSTIPESLYTHWKQTVFYMEDYLTLKTGEEIFGTIGMRPNAKN-WDRDF

Parental  TVDLDFKGQLCETSVSNDYKM
          T..LDF.G.LC..S.S.DY.M
Retrocopy TINLDFRGHLCDLSCSTDYRM

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	13.41 RPM	39.70 RPM
SRP007412_cerebellum	15.41 RPM	25.24 RPM
SRP007412_heart	28.65 RPM	0.03 RPM
SRP007412_kidney	15.82 RPM	0.44 RPM
SRP007412_liver	15.48 RPM	0.03 RPM
SRP007412_testis	10.43 RPM	1.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2313 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2313 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2313 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3406
Gorilla gorilla	retro_ggor_2305
Pongo abelii	retro_pabe_2804
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,