RetrogeneDB ID: retro_ggor_3024

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:63276574..63277752(-)
• 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_3024
AGCTTTGGAGACAAGTATCGAGATAGTTATGATTCAGACCGGTATCACGATGGGTATCAGGATGGGTATTGGGATGGCCC
ACACTGGGATATGGATTGATGTGGCAGCCAGGATCGCTATGATGACCAAGGCAGCACAGACTATGATAGACGCTATGATT
CCCGGATAGGCAGTGGCAGAAGGGCATTTGGCAGTGGGTGCCACAGGGATGATGACTATAGAGGAGGCGGGACTGGCTAT
GAAGACCAATAAGACAGACAGGATGATCGGTCATGGAACTCCAGAGATGATTACTCTCGGGATGATTATATGGGTGATGA
TAGAGGTCCCTCCCAAAGACCCAAACTGACTCTAAAGCCTCGGAGTGCTCCTAAGGAAGATGATTCCTCTGCTAGTACCT
CCCAGTCCAGTAGAGGTGCTTCTATCTTTGGAGGGGCAAAGCCCGTTGACACAGCTGCTAGAGAAAGAGAAGTAGAAGAA
CAGCTACAGAAGGAACACGAGAAGTTGCAGCATCAGCTGGATGAGCCAAAACTAGAACGACGGCCTCGGGAGAGACACCC
AAGCTGACAAAGTGAAGAAACTCAGGAACGGGAACAGTTGAGGACAGGAAGTGAGTCATTGCAGACTGGGACCTCCACCA
CATCCGGCAGAAATGCACGAAGGAGAGTGAGTGAGAAGTCACTAGAAAATGAAACACTCAATAAGGAGGAAGACTGTCAC
TCTCCAACTTCTAAACCTCCCAAACCTGATCAGTCCCTAAAGGTAATGCCAGCCCCTCCACCAAAGGAGAATGGTTGGGT
GAAGTGAAGTTCTAACCCTCCTGCTCAATCTCAGAGCTCAGACACAGAGCAGCAATCCCCTACAATTGGTGGGGTAAAGT
AGCTCCAGCTTAACCATCTGAGTAAGGACTAGCAAGGAAAGACGAAAATGAAGTAGATGGGATGAATATCCCAAAAGGCC
AAACTGGGAATTCTAGCCATGGTCCAGGAGAGGGAGGGAACAAAGACCACTCGAAGGAGTCAGATAGGAAAGATGACAAA
AAGGATAAAGACTCCAGATCTGCACCTGAGCCAAACAAACCTGAGGAAAATCCAGCTTCCAAGTTCAGTTCTGCAAGGAA
GTATGCTGCTCTCTCCATTGATGGTGAAGATAAAAATGAGGGAGAAGACTAAGCCGAA

Alignment

ORF - retro_ggor_3024 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.23 %
• Parental protein coverage: 64.32 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFGDKYRDRYDSDRYRDGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAFGSGYRRD
          SFGDKYRD.YDSD.............P..DMD..G..DRYDD.GS.DYDR.YDSRIGSGRRAFGSG..RD
Retrocopy SFGDKYRDSYDSDXXXXXXXXXXXXXPHWDMD*CGSQDRYDDQGSTDYDRRYDSRIGSGRRAFGSGCHRD

Parental  DDYRGGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTSQSTRAA
          DDYRGGG..YED..DR.DDRSW.SRDDYSRDDY..DDRGP.QRPKL.LKPRS.PKEDDSSASTSQS.R.A
Retrocopy DDYRGGGTGYEDQ*DRQDDRSWNSRDDYSRDDYMGDDRGPSQRPKLTLKPRSAPKEDDSSASTSQSSRGA

Parental  SIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQERERSRTGSESSQTG
          SIFGGAKPVDTAAREREVEE.LQKE.EKLQ.QLDEPKLERRPRERHPS..SEETQERE..RTGSES.QTG
Retrocopy SIFGGAKPVDTAAREREVEEQLQKEHEKLQHQLDEPKLERRPRERHPS*QSEETQEREQLRTGSESLQTG

Parental  TSTTSGRNARRRESEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWVKRSSNPPARSQSS
          TSTTSGRNARRR.SEKSLENETLNKEEDCHSPTSKPPKPDQ.LKVMPAPPPKEN.WVK.SSNPPA.SQSS
Retrocopy TSTTSGRNARRRVSEKSLENETLNKEEDCHSPTSKPPKPDQSLKVMPAPPPKENGWVK*SSNPPAQSQSS

Parental  DTEQQSPTSGG-GKVAPAQPSEEGPGRKDENKVDGMNAPKGQTGNSSRGPGDGGNRDHWKESDRKDGKKD
          DTEQQSPT.GG.GKVAPA.PSE.G..RKDEN.VDGMN.PKGQTGNSS.GPG.GGN.DH.KESDRKD.KKD
Retrocopy DTEQQSPTIGG<GKVAPA*PSE*GLARKDENEVDGMNIPKGQTGNSSHGPGEGGNKDHSKESDRKDDKKD

Parental  QDSRSAPEPKKPEENPASKFSSASKYAALSVDGEDENEGEDYAE
          .DSRSAPEP.KPEENPASKFSSA.KYAALS.DGED.NEGED.AE
Retrocopy KDSRSAPEPNKPEENPASKFSSARKYAALSIDGEDKNEGED*AE

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	0.03 RPM	78.11 RPM
SRP007412_testis	0.00 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_3024 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3024 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4848
Pongo abelii	retro_pabe_3768
Macaca mulatta	retro_mmul_2589

---

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,