RetrogeneDB ID: retro_ggor_1144

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 15:23484202..23484735(+)
• Located in intron of: ENSGGOG00000001602

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF4
• Ensembl ID: ENSGGOG00000015149
• Aliases: None
• Description: None

Sequence

>retro_ggor_1144
GTGAATTCCAGACAAGCCTGAGCATTCCCTATAGCCAGAGAAGGAGGCCCAACACCTAACATAGCCTTGGATGCAGAACT
GATAGAACTTGGGGAAAGTGATGAAGTAGTTGACCTCACCTGTGAATCTCTAGCACCTGTAGTGATTGACCTAACTCACC
GTGACTCTGTAGTGATTATTGAACAAAGGAGGAGGCCAAGAGCAAACACAAGGCCACTCCAAGACCACACTGGCAGTTGT
GTGGTGAACACTGATGAGGAGGGAGTGAAAAGGGACAGAGATGTATGTATAACCAACAGTGCCCACCATAATTCCCTGCA
AAAGAAATTTTTTTGTCATATACTACCTGGTTATATTCAGTGTCAAGTTTGCATGGATGGATGCTCAGAGATTGAACTTA
GTATACAACACATCTACTCTATAGAATGTGGCCACATCTGTAGTCAGTGCTTCTGCACTTCCTTTACACATACTAACACT
GCCCAATTTGTTTGAAAAAAATCAGCCTCCATCAGTATCACTGCATTTATATA

Alignment

ORF - retro_ggor_1144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.46 %
• Parental protein coverage: 94.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  INSRQ--AQKRTREATSTPEISLEAEPIELVETAGDEIVDLTCESLEPVVVDLTHNDSVVIVDERRRPRR
          .NSRQ..A....RE...TP.I.L.AE.IEL.E...DE.VDLTCESL.PVV.DLTH.DSVVI...RRRPR.
Retrocopy VNSRQA*AFPIAREGGPTPNIALDAELIELGES--DEVVDLTCESLAPVVIDLTHRDSVVIIEQRRRPRA

Parental  NARRLPQDHADSCVVSSDDEELSRDRDVYVTTHTPRNARDEGATGLRPSGTVSCPICMDGYSEIVQNGRL
          N.R.L.QDH..SCVV..D.E...RDRDV..T.....N............G...C..CMDG.SEI......
Retrocopy NTRPL-QDHTGSCVVNTDEEGVKRDRDVCITNSAHHNSLQKKFFCHILPGYIQCQVCMDGCSEIELSIQH

Parental  IVSTECGHVFCSQCLRDSLKNANT-CPTCRKKINHKRYHPIYI
          I.S.ECGH..CSQC...S....NT.CP.C.KKI....YH.IYI
Retrocopy IYSIECGHI-CSQCFCTSFTHTNT<CPICLKKISLHQYHCIYI

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	0.34 RPM	51.65 RPM
SRP007412_cerebellum	0.35 RPM	62.13 RPM
SRP007412_heart	0.09 RPM	13.29 RPM
SRP007412_kidney	0.53 RPM	81.66 RPM
SRP007412_liver	0.29 RPM	27.17 RPM
SRP007412_testis	0.31 RPM	67.34 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_1144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1144 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1240
Sus scrofa	retro_sscr_181
Canis familiaris	retro_cfam_25
Equus caballus	retro_ecab_33

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014366	1 retrocopy	retro_amel_77,
Canis familiaris	ENSCAFG00000014856	1 retrocopy	retro_cfam_25,
Equus caballus	ENSECAG00000024877	1 retrocopy	retro_ecab_33,
Homo sapiens	ENSG00000063978	1 retrocopy	retro_hsap_319,
Gorilla gorilla	ENSGGOG00000015149	2 retrocopies	retro_ggor_1144 , retro_ggor_345,
Loxodonta africana	ENSLAFG00000007382	1 retrocopy	retro_lafr_44,
Microcebus murinus	ENSMICG00000001767	1 retrocopy	retro_mmur_1265,
Mus musculus	ENSMUSG00000029110	1 retrocopy	retro_mmus_522,
Nomascus leucogenys	ENSNLEG00000000160	2 retrocopies	retro_nleu_1713, retro_nleu_37,
Oryctolagus cuniculus	ENSOCUG00000004998	2 retrocopies	retro_ocun_1566, retro_ocun_162,
Otolemur garnettii	ENSOGAG00000010776	1 retrocopy	retro_ogar_2121,
Pongo abelii	ENSPPYG00000025865	2 retrocopies	retro_pabe_1240, retro_pabe_36,
Pteropus vampyrus	ENSPVAG00000017017	1 retrocopy	retro_pvam_167,
Ictidomys tridecemlineatus	ENSSTOG00000011101	2 retrocopies	retro_itri_1108, retro_itri_171,
Tarsius syrichta	ENSTSYG00000011244	1 retrocopy	retro_tsyr_1606,