RetrogeneDB ID: retro_ggor_1739

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:91017014..91017532(+)
• Located in intron of: ENSGGOG00000010989

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000177350
• Ensembl ID: ENSGGOG00000002932
• Aliases: None
• Description: None

Sequence

>retro_ggor_1739
AAAGTAGTGGTCATGTCCTGTGAGGACATCAACATTTCTGGCAGTTTCTACAGAAACAAGTTAAAGTATCTAGCCTTCTT
CTGCAAGCGGACAAGCACCAACCCTTCCCAAGGACCCTACCATTTATGGGTCCCCAGCCACATCTTTTGGCAGACCACCT
GCGGTAGGCTGCCCCACAAGACCAAGCAAGGCTAGGCTGCCCTAGATCACCTCAAGGTGTTTGATAGAATCCCCTTGCCA
TATGACAAGAAAAAGCAGATGGTGGTTTCTGCCACCCTCGAGGTTGTACGTCCGAAGCCTTGAAGAAAGTTTGCCTACCT
GGGGCACTGGGCTCAGAAGGTTGACTGGAAATACCAGGCAATGACAGCCACCATGGGGGAGAAGAGGAAGGTCTATTATC
AGAAGATCTGTTACCAGAAGAAAAACAGCTCATGAGGCTATAGGAAAAGGCTGAAAAGAACATAGAGACGAACATTGACA
AATACACGAAGGTTCTCAAGGCCCACAGACTCCTAGTC

Alignment

ORF - retro_ggor_1739 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.11 %
• Parental protein coverage: 84.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVVVVRCEGINISGNFYRNKLKYLAFLRKRMNTNPSRGPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDR
          KVVV..CE.INISG.FYRNKLKYLAF..KR..TNPS.GPYH...PS.IFW.T..G.LPHKTK.G.AALD.
Retrocopy KVVVMSCEDINISGSFYRNKLKYLAFFCKRTSTNPSQGPYHLWVPSHIFWQTTCGRLPHKTKQG*AALDH

Parental  LKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLGRLAHEVGWKYQAVTATLEEKRK-EKAKIHYRK
          LKVFD.IP.PYDKKK.MVV.A.L.VVR.KP.RKFAYLG..A..V.WKYQA.TAT..EKRK....KI.Y.K
Retrocopy LKVFDRIPLPYDKKKQMVVSATLEVVRPKP*RKFAYLGHWAQKVDWKYQAMTATMGEKRKVYYQKICYQK

Parental  K-KQLMRLRKQAEKNVEKKIDKYTEVLKTHGLLV
          K.KQLMRL...AEKN.E..IDKYT.VLK.H.LLV
Retrocopy K<KQLMRL*EKAEKNIETNIDKYTKVLKAHRLLV

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	202.37 RPM
SRP007412_cerebellum	0.24 RPM	267.43 RPM
SRP007412_heart	0.16 RPM	188.53 RPM
SRP007412_kidney	0.49 RPM	447.28 RPM
SRP007412_liver	0.18 RPM	505.64 RPM
SRP007412_testis	0.52 RPM	207.51 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_1739 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1739 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2200
Macaca mulatta	retro_mmul_924
Callithrix jacchus	retro_cjac_2755

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 109 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005296	3 retrocopies	retro_btau_1251, retro_btau_719, retro_btau_789,
Callithrix jacchus	ENSCJAG00000000072	16 retrocopies	retro_cjac_1130, retro_cjac_1706, retro_cjac_182, retro_cjac_197, retro_cjac_1997, retro_cjac_2170, retro_cjac_2322, retro_cjac_2467, retro_cjac_2468, retro_cjac_2665, retro_cjac_2699, retro_cjac_2755, retro_cjac_3009, retro_cjac_664, retro_cjac_941, retro_cjac_972,
Cavia porcellus	ENSCPOG00000012417	2 retrocopies	retro_cpor_1000, retro_cpor_888,
Equus caballus	ENSECAG00000015832	3 retrocopies	retro_ecab_388, retro_ecab_653, retro_ecab_773,
Erinaceus europaeus	ENSEEUG00000014071	6 retrocopies	retro_eeur_168, retro_eeur_310, retro_eeur_315, retro_eeur_484, retro_eeur_562, retro_eeur_618,
Echinops telfairi	ENSETEG00000017076	2 retrocopies	retro_etel_46, retro_etel_853,
Felis catus	ENSFCAG00000009194	4 retrocopies	retro_fcat_1197, retro_fcat_1649, retro_fcat_324, retro_fcat_548,
Gorilla gorilla	ENSGGOG00000002932	11 retrocopies	retro_ggor_12, retro_ggor_1739 , retro_ggor_214, retro_ggor_2271, retro_ggor_2737, retro_ggor_334, retro_ggor_6, retro_ggor_615, retro_ggor_627, retro_ggor_846, retro_ggor_869,
Loxodonta africana	ENSLAFG00000016213	3 retrocopies	retro_lafr_1160, retro_lafr_576, retro_lafr_810,
Myotis lucifugus	ENSMLUG00000004945	10 retrocopies	retro_mluc_1015, retro_mluc_1342, retro_mluc_1836, retro_mluc_1894, retro_mluc_2219, retro_mluc_2221, retro_mluc_2427, retro_mluc_2471, retro_mluc_2506, retro_mluc_675,
Mustela putorius furo	ENSMPUG00000002604	3 retrocopies	retro_mputfur_1418, retro_mputfur_853, retro_mputfur_935,
Mus musculus	ENSMUSG00000074129	3 retrocopies	retro_mmus_1129, retro_mmus_1334, retro_mmus_20,
Otolemur garnettii	ENSOGAG00000004625	7 retrocopies	retro_ogar_1496, retro_ogar_211, retro_ogar_2254, retro_ogar_3148, retro_ogar_54, retro_ogar_596, retro_ogar_612,
Ochotona princeps	ENSOPRG00000001194	3 retrocopies	retro_opri_316, retro_opri_764, retro_opri_806,
Procavia capensis	ENSPCAG00000004086	4 retrocopies	retro_pcap_163, retro_pcap_290, retro_pcap_415, retro_pcap_416,
Pongo abelii	ENSPPYG00000010251	1 retrocopy	retro_pabe_148,
Pteropus vampyrus	ENSPVAG00000010958	3 retrocopies	retro_pvam_129, retro_pvam_625, retro_pvam_771,
Rattus norvegicus	ENSRNOG00000020618	10 retrocopies	retro_rnor_1073, retro_rnor_1112, retro_rnor_1212, retro_rnor_1292, retro_rnor_1357, retro_rnor_1742, retro_rnor_564, retro_rnor_593, retro_rnor_665, retro_rnor_988,
Sus scrofa	ENSSSCG00000003166	4 retrocopies	retro_sscr_290, retro_sscr_300, retro_sscr_392, retro_sscr_743,
Tarsius syrichta	ENSTSYG00000008791	4 retrocopies	retro_tsyr_1363, retro_tsyr_437, retro_tsyr_620, retro_tsyr_920,
Tursiops truncatus	ENSTTRG00000005485	7 retrocopies	retro_ttru_1304, retro_ttru_1736, retro_ttru_629, retro_ttru_735, retro_ttru_833, retro_ttru_971, retro_ttru_995,