RetrogeneDB ID: retro_ggor_1882

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:122296838..122298133(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSGGOG00000013695
• Aliases: None
• Description: None

Sequence

>retro_ggor_1882
AGGGACGATCGTTCTTTTGGCCATGAGAGAAATCGGGATTTTGACAAAACAAATACAGACTGGAGGGCTCGTCCTGTCAC
AGACAGCTTGGATGACTACTCGCCTAGAAGAGGTGATGATTGCTTTGGAGACAAGTATCAAGATCGTTATGATTCAGACC
GGTATCGCGATGGGTATCGGGAGGGGTATCGGGATGGCCCACGCTGGGATATGGATCGATATGGCGGCCAGGATTGCTAT
GATGACCCACGCAGCAGACACTATGATAGAGACTATGATTCCCAGATAGGCAATGGCAGAAGAGCATTTGGTAGTGGGTA
CCGCAGGGATAATGACTACAGAGGAGGCAGGGACGGCTCTGAAGACCGATACAACAGACGGGATGATCGGTCATGGAGCT
CCAGAGATGATTACACTTGGGATGATTATAGGTGTGATGATAGAGGTCCCCGCAAAGACCCAAACTGAATCTAAAGCTTT
GGAGTACTCCCAAGGAAGATGATTCCTCTGTTAGTACCTCCCAGTCCAGTCGAGCTGCTTCTATCTTTGGAGGGGCAAAG
CCCGTTGACACAGCTGCTAGAGAAAGAGAAGTAGAAGAAATGCTACAGAACAAGAGAAGTTGCAGCGTCAGCTGGATGAG
CCATAACTAGAACGACGACCTCGGGAGAGACACCCAAGCTGGCAAAGTGAAGAAACTCAAGAATGGAACGGTCGCGGACA
GGAAGTGAGTCATCGCAGACTGAGACCTCCGCCACATCCAGCAGAAATGCACGAAGGAAAGAGTGAGAAGTCTCTAGAAA
ATGAAACACTCAATAAGGAGGAAGATTGTCACTCTCTAACTTCTAAACGTCTCAAACCTGATCCTACCAGACCCAAAGGT
AATGCCAGCCCCTCCACCAAAGGAGAATGCTTCGGTGAAGTGAAGTTCTAACCCTCCTGCTCCATCTCAGAGCTCAGACA
CAGAGCAGCAATCCCCTACAAGTGGTGGGGGAAAAGTAGCTCCAGCTCGATCATCTGAGGAAGGACCAGCAAAGAAAGAT
GAAAATAAAGTGGATGGGATGAAAGTCCCAAAAGGTCAAATTGGGAACTCTAGCTGTGGTCCAGGAGATGGAGGGAACAA
AGACCACTGAAAGGAGTCAGATAGGAAATATGGCAAAAAGGATCAAGACTCCAGATCTGCACCTGAGCCAAAGAAACCTG
AGGAAAATCCAGCTTCCAAGTTCAGTTCTGCAAGCAAGTATGCTGCTGTCTCCGTTTCTGGTGAAGATGAAAACAAGGGA
GAAGATTACGCCGAG

Alignment

ORF - retro_ggor_1882 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.8 %
• Parental protein coverage: 70.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RDDRSFGRDRNRDSDKTDTDWRARPATDTFDDYPPRRGDDSFGDKYRDRYDSDRYRDGYRDGYRDGPRRD
          RDDRSFG..RNRD.DKT.TDWRARP.TD..DDY.PRRGDD.FGDKY.DRYDSD.............PR.D
Retrocopy RDDRSFGHERNRDFDKTNTDWRARPVTDSLDDYSPRRGDDCFGDKYQDRYDSDXXXXXXXXXXXXXPRWD

Parental  MDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAFGSGYRRDDDYRGGGDRYEDRYDRRDDRSWSSRDDYSR
          MDRYGG.D.YDD..SR.YDR.YDS.IG.GRRAFGSGYRRD.DYRGG.D..EDRY.RRDDRSWSSRDDY..
Retrocopy MDRYGGQDCYDDPRSRHYDRDYDSQIGNGRRAFGSGYRRDNDYRGGRDGSEDRYNRRDDRSWSSRDDYTW

Parental  DDYRRDDRGP-PQRPKLNLKPRSTPKEDDSSASTSQSTRAASIFGGAKPVDTAARE-REVEERLQKEQEK
          DDYR.DDRGP.PQRPKLNLK..STPKE.D.S.........A....G.......A...R....R...EQEK
Retrocopy DDYRCDDRGP<PQRPKLNLKLWSTPKE-DDSSVSTSQSSRAASIFGGAKPVDTAAR<RKRSRRNATEQEK

Parental  LQRQLDEPKLERRPRERHPSWRSEETQE-RERSRTGSESSQTGTSTTSGRNARRRE-SEKSLENETLNKE
          LQRQLDEP.LERRPRERHPSW.SEETQE..ERSRTGSESSQT.TS.TS.RNA.RR..SEKSLENETLNKE
Retrocopy LQRQLDEP*LERRPRERHPSWQSEETQE<MERSRTGSESSQTETSATSSRNA-RRK>SEKSLENETLNKE

Parental  EDCHSPTSKPPKPDQ-PLKVMPAPPP-KENAWVKRSSNPPARSQSSDTEQQSPTSGGGKVAPAQPSEEGP
          EDCHS.TSK..KPD..P.......PP.KENA.VK.SSNPPA.SQSSDTEQQSPTSGGGKVAPA..SEEGP
Retrocopy EDCHSLTSKRLKPDP>PDPKVMPAPPPKENASVK*SSNPPAPSQSSDTEQQSPTSGGGKVAPARSSEEGP

Parental  GRKDENKVDGMNAPKGQTGNSSRGPGDGGNRDHWKESDRKDGKKDQDSRSAPEPKKPEENPASKFSSASK
          ..KDENKVDGM..PKGQ.GNSS.GPGDGGN.DH.KESDRK.GKKDQDSRSAPEPKKPEENPASKFSSASK
Retrocopy AKKDENKVDGMKVPKGQIGNSSCGPGDGGNKDH*KESDRKYGKKDQDSRSAPEPKKPEENPASKFSSASK

Parental  YAALSVDGEDENEGEDYAE
          YAA.SV.GEDEN.GEDYAE
Retrocopy YAAVSVSGEDENKGEDYAE

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	105.16 RPM
SRP007412_cerebellum	0.00 RPM	94.32 RPM
SRP007412_heart	0.00 RPM	51.50 RPM
SRP007412_kidney	0.00 RPM	153.86 RPM
SRP007412_liver	0.00 RPM	78.11 RPM
SRP007412_testis	0.10 RPM	171.98 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_1882 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1882 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2283
Macaca mulatta	retro_mmul_1428

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012023	2 retrocopies	retro_amel_1107, retro_amel_559,
Canis familiaris	ENSCAFG00000007117	2 retrocopies	retro_cfam_1447, retro_cfam_936,
Choloepus hoffmanni	ENSCHOG00000001608	2 retrocopies	retro_chof_1310, retro_chof_366,
Callithrix jacchus	ENSCJAG00000018176	2 retrocopies	retro_cjac_1717, retro_cjac_2001,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Homo sapiens	ENSG00000063046	7 retrocopies	retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla	ENSGGOG00000005284	1 retrocopy	retro_ggor_1598,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882 , retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Nomascus leucogenys	ENSNLEG00000017727	3 retrocopies	retro_nleu_2371, retro_nleu_2601, retro_nleu_721,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus	ENSSTOG00000006800	1 retrocopy	retro_itri_604,
Tupaia belangeri	ENSTBEG00000005423	2 retrocopies	retro_tbel_2363, retro_tbel_4167,
Tarsius syrichta	ENSTSYG00000012880	1 retrocopy	retro_tsyr_452,