RetrogeneDB ID: retro_ggor_1986

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:156003415..156005006(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000070756
• Ensembl ID: ENSGGOG00000006785
• Aliases: None
• Description: None

Sequence

>retro_ggor_1986
AATCCGGACAAATCCATTGATAATAAAACACTGTATGATACATTTTCTGCTTTTTGTAACATCGTTTCATGTAAAGTGGT
TGGTGATGAAAATGGTTCCAAGGGCTATGGATTTGTACGCTTTGAGATGCAGGAAGCAGCTGAAAGAGGTATTGAAAAAA
ATGAATGGAATGCTCCTAAATGGTCGCAAAGTATTTGTTGGACGATTTAAGTCTCGTAAAAAACGGGAAACTGAACTTGG
AGCTAGGGCAAAAGAGTTCACCAATGTTTACATCAAGAATTTTGGAGAAGACATGGATGATGAGCACTTTAAGGATCTCT
TTGGCAAGTTTGGCCCTGCCGTAAGTGTGAAAGTAATGACTGATGAAGGTGGAAAATCCGAAGGATTTGGATTTGTAAGC
TTTGAAAGGCATGAGGATGCACAGAAAGCTGTGGATGAGATTAATGGAAATGGAGCTCAATGGAAAACAAATTTATGTTG
GTCGAGCTCAGAAAAAGGTGGAACAGCAGACGGAACTTAAGTGCAAATTTGAACAGATGAAGCAAGATAGGATTACCAGG
TACTAGGGTGTTAATCTTTATGTGAAAAATCTTGATGATGGTATTGATGATGAACGTCTCCAGAGATGTTTTCTCCATTT
GGTATAATCACTAGTGCAAAGGTTGGAGGGTGGTCGCAGCAAGGGTTTGGTTTTGTATGTTTCTCCTCCCCAGAATAAGC
CACTAAAGCAGTTACAGAAATGAATGGTAGAATTGTAGCCACAAAGTCATTGTATTTAGCTTTAGCTCAGCGCAAAGGAG
AGTGCCAGGCTCACCTCACTAACCAGTATATGCAGAGAATGGCAAGTGTATGAGCTGTGCCCAACCCTGTAATCAACCCC
TATCAGCTAGCACCTCCTTCAGGTTTCTTAATGGCAGCTATCTCACAGTCTCAGAACTGTGCTGCATACCCTCCTCCTAG
CCAAATTGCTCAGCTAAGACCAAGTCCTCACTGGACTGCTCAGGGTGCCAGACCTCATCCATTCCAAAATATGCCCGGTG
CTACCCGCCCAGCTGCTCCTAGACCACCATTTAGTACTATGAGACCAGCTTCTTCACAGGTTCCACAAGTCATGTCAACA
CAGTGTGTTGCTAACACATTAACACAGACAATGGGTCCATGTCCTGCAGCTGCAGCTGCTGCAGCTACTCCTGCTATCTG
CACTGTTCCACAGTATAAATATGCTGCAGGACTTCGCAATCCTCAGCAACATCTTAATGCACAGCCACAAGTTACAATGC
AACAGCCTGCTGTTCATGTACAAGGTCAGGAACCTTTGACTGCTTCCATGTTGGCATCTGCCCCTCCTCAAGAGGGAAAG
CAAATGTCGGGTGAATGGCTGTTTCCTTTTATTCAAGCCTTGCACCCTACTCTTGCTAGTAAAATCACTGGCATATTGTT
GGAGATTGATAATTCAGAAGTTCTTCATATGCTCGAGTCTCCAGAGTTACTCCGTTATAAAGTTGATGAAGCTGTAGCTA
TACTACAAGTCCGTCAAGTTAAAGAGGCTTCCCAGAAAGCAGTTAACAGCGCCACTGGTGTTCCAACTGTT

Alignment

ORF - retro_ggor_1986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.54 %
• Parental protein coverage: 93.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK-MNGMLLNDRKVFVGRF
          N.DKSIDNK.LYDTFSAF.NI.SCKVV.DENGSKGYGFV.FE.QEAAER.IEK.MNGMLLN.RKVFVGRF
Retrocopy NPDKSIDNKTLYDTFSAFCNIVSCKVVGDENGSKGYGFVRFEMQEAAERGIEK>MNGMLLNGRKVFVGRF

Parental  KSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHED
          KSRK.RE.ELGARAKEFTNVYIKNFGEDMDDE..KDLFGKFGPA.SVKVMTDE.GKS.GFGFVSFERHED
Retrocopy KSRKKRETELGARAKEFTNVYIKNFGEDMDDEHFKDLFGKFGPAVSVKVMTDEGGKSEGFGFVSFERHED

Parental  AQKAVDEMNGK-ELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRK
          AQKAVDE.NG..ELNGKQIYVGRAQKKVE.QTELK.KFEQMKQDRITRY.GVNLYVKNLDDGIDDERL..
Retrocopy AQKAVDEINGN>ELNGKQIYVGRAQKKVEQQTELKCKFEQMKQDRITRY*GVNLYVKNLDDGIDDERLQR

Parental  -EFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQ
          ..FSPFG.ITSAKV...G....GFGFVCFSSPE.ATKAVTEMNGRIVATK.LY.ALAQRK.E.QAHLTNQ
Retrocopy <MFSPFGIITSAKV--GGWSQQGFGFVCFSSPE*ATKAVTEMNGRIVATKSLYLALAQRKGECQAHLTNQ

Parental  YMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMP
          YMQRMASV.AVPNPVINPYQ.APPSG..MAAI.Q.QN.AAY.PPSQIAQLRPSP.WTAQGARPHPFQNMP
Retrocopy YMQRMASV*AVPNPVINPYQLAPPSGFLMAAISQSQNCAAYPPPSQIAQLRPSPHWTAQGARPHPFQNMP

Parental  GAIRPAAPRPPFSTMRPASSQVPRVMSTQRVANTSTQTMGPRPAAAAAAATPAVRTVPQYKYAAGVRNPQ
          GA.RPAAPRPPFSTMRPASSQVP.VMSTQ.VANT.TQTMGP.PAAAAAAATPA..TVPQYKYAAG.RNPQ
Retrocopy GATRPAAPRPPFSTMRPASSQVPQVMSTQCVANTLTQTMGPCPAAAAAAATPAICTVPQYKYAAGLRNPQ

Parental  QHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNS
          QHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQE.KQM.GE.LFP.IQA.HPTLA.KITG.LLEIDNS
Retrocopy QHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEGKQMSGEWLFPFIQALHPTLASKITGILLEIDNS

Parental  ELLHMLESPESLRSKVDEAVAVLQAHQAKEAAQKAVNSATGVPTV
          E.LHMLESPE.LR.KVDEAVA.LQ..Q.KEA.QKAVNSATGVPTV
Retrocopy EVLHMLESPELLRYKVDEAVAILQVRQVKEASQKAVNSATGVPTV

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	0.10 RPM	63.73 RPM
SRP007412_cerebellum	0.04 RPM	77.26 RPM
SRP007412_heart	0.00 RPM	27.45 RPM
SRP007412_kidney	0.04 RPM	197.74 RPM
SRP007412_liver	0.03 RPM	155.89 RPM
SRP007412_testis	1.04 RPM	835.64 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_1986 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1986 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2373

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000348	1 retrocopy	retro_amel_1650,
Choloepus hoffmanni	ENSCHOG00000008178	1 retrocopy	retro_chof_2531,
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus	ENSCPOG00000012917	1 retrocopy	retro_cpor_1324,
Dasypus novemcinctus	ENSDNOG00000008718	2 retrocopies	retro_dnov_1530, retro_dnov_2259,
Felis catus	ENSFCAG00000001874	1 retrocopy	retro_fcat_1927,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Gorilla gorilla	ENSGGOG00000004002	3 retrocopies	retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Gorilla gorilla	ENSGGOG00000006785	1 retrocopy	retro_ggor_1986 ,
Myotis lucifugus	ENSMLUG00000012245	1 retrocopy	retro_mluc_579,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Tarsius syrichta	ENSTSYG00000004229	2 retrocopies	retro_tsyr_1743, retro_tsyr_273,