RetrogeneDB ID: retro_ggor_2305

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:161851971..161852855(-)
• Located in intron of: ENSGGOG00000011744

Retrocopy information

• Ensembl ID: ENSGGOG00000027930
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRMT1
• Ensembl ID: ENSGGOG00000000503
• Aliases: None
• Description: None

Sequence

>retro_ggor_2305
TTCGGCAACTCCATGTTTCACAACCGGCACGTCTTTAAAGACAAGGTGGTGCTGGATGTGGGCTCGGACACAAGCATCCT
CTGCATGTTCGCCGCCAAGGCCGGGCCCGCAAGGTCATCAGCATCGAGTGTTCCAGTAGGTCTGATTATGCGGTGAAGAT
TGTCAAAGCCAACAAGTTAGACCACTTGGTGACCATCACCAAGGGGAAGGTGGAGGAGATAGAGCTCCCGGTGGAAAAGG
TGGACGTCATCATCAGCAAGTGGATGGGCTAACTGCCTCTTCTACGAGTCCATGCTCAACACTGTGCTCTATGCCCGGAC
AAGTGGCTGGCGCCCAATAGCCTCATCTTCCCAGACCGGGCCACACTGTATGTGACGGCCACCGAGGACCGGCAGTACAA
AGACTACAAGATCCACTGGTGGGAGAACGTTTATGCCTTCGATATATCTTGCATCAAAGATGTGGCCATCAAGGAAACCC
TAGTGGATGTGGTGGACCTCAAACAGCTGGTCACCAACGCCTGCCTCATAAAGGACGTAGACATCTACACCGTCAAGGTG
GAAGACCTGACCTTCACCTCCCCGTTCTGCCTGCAAGTGAAGCAGAATGACTACGTGCACGCCCAGGTGGCCTACTTCAA
CGTCGAGTTTACGCACTGCCACAAGAGGACCGGCTTCTCCACCATACCCGAGTCCCTGTACACGCACTGGAAGCAGACTG
TGTTCTACATGGAGGACTACCTGACCTTGAAGACGGGCGAGGAGATCTTCGGCACCATCGGCATGCGGCCCAACGCCAAG
AACAACTGGGACCTGGACTTCACCATCAACCTAGATTTCAGGGGCCATCTGTGCGACCTGTCCTGCTCCACAGACTACAG
GATG

Alignment

ORF - retro_ggor_2305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.92 %
• Parental protein coverage: 79.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YRNSMFHNRHLFKDKVVLDVGSGTGILCMFAAKAG-ARKVIGIECSSISDYAVKIVKANKLDHVVTIIKG
          ..NSMFHNRH.FKDKVVLDVGS.T.ILCMFAAKAG.ARKVI.IECSS.SDYAVKIVKANKLDH.VTI.KG
Retrocopy FGNSMFHNRHVFKDKVVLDVGSDTSILCMFAAKAG<ARKVISIECSSRSDYAVKIVKANKLDHLVTITKG

Parental  KVEEVELPVEKVDIIISEWMG-YCLFYESMLNTVLYAR-DKWLAPDGLIFPDRATLYVTAIEDRQYKDYK
          KVEE.ELPVEKVD.IIS.WMG..CLFYESMLNTVLYAR.DKWLAP..LIFPDRATLYVTA.EDRQYKDYK
Retrocopy KVEEIELPVEKVDVIISKWMG>NCLFYESMLNTVLYAR<DKWLAPNSLIFPDRATLYVTATEDRQYKDYK

Parental  IHWWENVYGFDMSCIKDVAIKEPLVDVVDPKQLVTNACLIKEVDIYTVKVEDLTFTSPFCLQVKRNDYVH
          IHWWENVY.FD.SCIKDVAIKE.LVDVVD.KQLVTNACLIK.VDIYTVKVEDLTFTSPFCLQVK.NDYVH
Retrocopy IHWWENVYAFDISCIKDVAIKETLVDVVDLKQLVTNACLIKDVDIYTVKVEDLTFTSPFCLQVKQNDYVH

Parental  ALVAYFNIEFTRCHKRTGFSTSPESPYTHWKQTVFYMEDYLTVKTGEEIFGTIGMRPNAKNNRDLDFTID
          A.VAYFN.EFT.CHKRTGFST.PES.YTHWKQTVFYMEDYLT.KTGEEIFGTIGMRPNAKNN.DLDFTI.
Retrocopy AQVAYFNVEFTHCHKRTGFSTIPESLYTHWKQTVFYMEDYLTLKTGEEIFGTIGMRPNAKNNWDLDFTIN

Parental  LDFKGQLCELSCSTDYRM
          LDF.G.LC.LSCSTDYRM
Retrocopy LDFRGHLCDLSCSTDYRM

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	0.14 RPM	95.76 RPM
SRP007412_cerebellum	0.16 RPM	101.96 RPM
SRP007412_heart	0.16 RPM	64.57 RPM
SRP007412_kidney	0.33 RPM	48.54 RPM
SRP007412_liver	0.21 RPM	32.44 RPM
SRP007412_testis	8.91 RPM	65.06 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2305 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2305 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3406
Pan troglodytes	retro_ptro_2313
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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003670	3 retrocopies	retro_cjac_1800, retro_cjac_1979, retro_cjac_764,
Danio rerio	ENSDARG00000010246	1 retrocopy	retro_drer_7,
Felis catus	ENSFCAG00000006081	1 retrocopy	retro_fcat_1762,
Homo sapiens	ENSG00000126457	1 retrocopy	retro_hsap_3406,
Gasterosteus aculeatus	ENSGACG00000004897	1 retrocopy	retro_gacu_2,
Gorilla gorilla	ENSGGOG00000000503	1 retrocopy	retro_ggor_2305 ,
Macaca mulatta	ENSMMUG00000003029	1 retrocopy	retro_mmul_2121,
Otolemur garnettii	ENSOGAG00000011938	2 retrocopies	retro_ogar_2471, retro_ogar_2929,
Rattus norvegicus	ENSRNOG00000026109	2 retrocopies	retro_rnor_1077, retro_rnor_2668,