RetrogeneDB ID: retro_ggor_1963

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:107710764..107711171(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL13
• Ensembl ID: ENSGGOG00000025427
• Aliases: None
• Description: 60S ribosomal protein L13 [Source:UniProtKB/TrEMBL;Acc:G3RUF5]

Sequence

>retro_ggor_1963
AGATGCAAGACCCAGCAAGCAAAAGCACACCACCATTGCCTATCATCCTGCATCTGGACCCATCTAGCCCATAGTAGGAT
ATCCCACAGGGAGATATCACACCAAAGTATAAGCTAGCAGAAGCTTCAGCTTAGAAGAGTTAAGGTGGCCAGCATCCACA
CGGTGACCCAGACCTTTGGTATCTGTGGATCCAAGGAGACATTAGAACAAGTCGAGTGAGTCCTGAAATGCCAGCAACTC
CAGTTGAAGGAGTACTGCTACAAGCTCATCCGCTTCCCCAGGAAGCCCTTGGACCCCACGAAGGAAGACAGCTCTGCTGA
ACTCAAATTGGCAACCCAGCTGACAGGACCAGTAATGTGCATATCAGTGTCTTCAAGGAGAAAGCCAGTGTCATCACCAA
GGAGAAG

Alignment

ORF - retro_ggor_1963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 78.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RRKARQAKARR-IAPRPASGPIRPIVRCPTVRYHTKVRAGRGFSLEELR-VAGIHKKVARTIGISVDP-R
          R.K..QAKA...IA..PASGPI.PIV..PT.RYHTKV.A.R.FSLEELR.VA.IH..V..T.GI.....R
Retrocopy RCKTQQAKAHH>IAYHPASGPI*PIVGYPTGRYHTKV*ASRSFSLEELR<VASIH-TVTQTFGICGSK>R

Parental  RRNKSTES-LQANVQRLKEYRSKLILFPRKPSAPKKGDSSAEELKLATQLTGPVMPIR-NVYKKEKARVI
          ..NKS.ES.L......LKEY..KLI.FPRKP..P.K.DSSA.ELKLATQLTGPVM.I...V.K.EKA.VI
Retrocopy H*NKSSES<LKCQQLQLKEYCYKLIRFPRKPLDPTKEDSSA-ELKLATQLTGPVMCIS<SVFK-EKASVI

Parental  TEEE
          T.E.
Retrocopy TKEK

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	0.43 RPM	118.40 RPM
SRP007412_cerebellum	1.42 RPM	160.19 RPM
SRP007412_heart	0.03 RPM	135.27 RPM
SRP007412_kidney	0.29 RPM	269.25 RPM
SRP007412_liver	0.16 RPM	385.09 RPM
SRP007412_testis	0.62 RPM	108.05 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_1963 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1963 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2824
Pan troglodytes	retro_ptro_1914

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 116 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017072	1 retrocopy	retro_acar_70,
Ailuropoda melanoleuca	ENSAMEG00000001111	5 retrocopies	retro_amel_1268, retro_amel_1319, retro_amel_188, retro_amel_411, retro_amel_802,
Bos taurus	ENSBTAG00000012044	2 retrocopies	retro_btau_716, retro_btau_817,
Canis familiaris	ENSCAFG00000019840	5 retrocopies	retro_cfam_1135, retro_cfam_1919, retro_cfam_2122, retro_cfam_565, retro_cfam_897,
Callithrix jacchus	ENSCJAG00000009672	5 retrocopies	retro_cjac_2607, retro_cjac_2961, retro_cjac_4054, retro_cjac_663, retro_cjac_747,
Cavia porcellus	ENSCPOG00000027348	4 retrocopies	retro_cpor_1014, retro_cpor_1192, retro_cpor_1242, retro_cpor_491,
Echinops telfairi	ENSETEG00000015057	4 retrocopies	retro_etel_1240, retro_etel_1382, retro_etel_1606, retro_etel_703,
Felis catus	ENSFCAG00000003338	4 retrocopies	retro_fcat_1946, retro_fcat_706, retro_fcat_852, retro_fcat_866,
Gorilla gorilla	ENSGGOG00000025427	6 retrocopies	retro_ggor_1548, retro_ggor_1963 , retro_ggor_2231, retro_ggor_2732, retro_ggor_562, retro_ggor_767,
Loxodonta africana	ENSLAFG00000004054	5 retrocopies	retro_lafr_659, retro_lafr_766, retro_lafr_827, retro_lafr_828, retro_lafr_829,
Microcebus murinus	ENSMICG00000008191	4 retrocopies	retro_mmur_249, retro_mmur_288, retro_mmur_779, retro_mmur_908,
Myotis lucifugus	ENSMLUG00000010950	6 retrocopies	retro_mluc_1431, retro_mluc_1436, retro_mluc_1549, retro_mluc_2022, retro_mluc_891, retro_mluc_991,
Macaca mulatta	ENSMMUG00000017928	7 retrocopies	retro_mmul_2021, retro_mmul_2150, retro_mmul_2350, retro_mmul_579, retro_mmul_593, retro_mmul_737, retro_mmul_781,
Monodelphis domestica	ENSMODG00000003663	4 retrocopies	retro_mdom_1001, retro_mdom_416, retro_mdom_439, retro_mdom_674,
Mus musculus	ENSMUSG00000000740	23 retrocopies	retro_mmus_1091, retro_mmus_1522, retro_mmus_1533, retro_mmus_1854, retro_mmus_2074, retro_mmus_2163, retro_mmus_2186, retro_mmus_2321, retro_mmus_2333, retro_mmus_2351, retro_mmus_25, retro_mmus_2668, retro_mmus_2718, retro_mmus_3097, retro_mmus_3274, retro_mmus_3453, retro_mmus_3489, retro_mmus_3500, retro_mmus_355, retro_mmus_3711, retro_mmus_692, retro_mmus_732, retro_mmus_863,
Ornithorhynchus anatinus	ENSOANG00000006729	1 retrocopy	retro_oana_78,
Otolemur garnettii	ENSOGAG00000026444	3 retrocopies	retro_ogar_1165, retro_ogar_1831, retro_ogar_1853,
Pteropus vampyrus	ENSPVAG00000015130	6 retrocopies	retro_pvam_1174, retro_pvam_1289, retro_pvam_1344, retro_pvam_228, retro_pvam_58, retro_pvam_616,
Rattus norvegicus	ENSRNOG00000015335	14 retrocopies	retro_rnor_1054, retro_rnor_1260, retro_rnor_158, retro_rnor_160, retro_rnor_1719, retro_rnor_1720, retro_rnor_1834, retro_rnor_1848, retro_rnor_2471, retro_rnor_2574, retro_rnor_2608, retro_rnor_2787, retro_rnor_2854, retro_rnor_682,
Sus scrofa	ENSSSCG00000024974	3 retrocopies	retro_sscr_1044, retro_sscr_725, retro_sscr_884,
Vicugna pacos	ENSVPAG00000000569	4 retrocopies	retro_vpac_310, retro_vpac_312, retro_vpac_576, retro_vpac_631,