RetrogeneDB ID: retro_ggor_2657

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:49227998..49228903(+)
• Located in intron of: ENSGGOG00000014572

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRIX1
• Ensembl ID: ENSGGOG00000004225
• Aliases: None
• Description: None

Sequence

>retro_ggor_2657
ATGGCGGCAACCAAGAGGAAACAGCATGGAGGCGTGGCAGTTCAGGCGAAGAACCCAGAAAGAAGCGAAAAAGAGGCCGA
GCAGCCAGCTAAGCTGGGTGCCACTGCAAAGGAGGTGGAAGAAGAAGATAGAGACTGGATCCCAGGCCCCGTTTGCAAGG
GGGAGTGAAAAAACAAGGAATGGATTTTCATCTTTTCTTCCAGAGGAATAAATAAATTTCAGAACAAGACATTTTATGCA
GGACTTGAGAATGTTGATGCCTCATTCTAAAGCAGATGCTAAAATGGATCGTAAGCATAAATAATTTGAGATTAGTGAGT
TCTGTGAAATGAAAAACTGTAATAAATGCATCTACTTTGAAGCTAAGAAAAAAACAGGATCTCTTTATGTAGCTTTCAAA
TTCACCTCATGGACCATCTGCTAAATTCCTTGTTCAAAATAGTCATAGCCTAGCTGAACTGAAGATGACTGGAAACCTTT
TGAAAGGTTCTTGCCCCTTTTGTCTTGACCCAGCTTTTGATGAATTACTACATTATGCTTTGTTAAAAGAACTCTTAATT
CAGATCTTTAGTACACCGTGGTATCATCCCAAAAGCCAACCATTCGTGGGCCGTGTGTTGACTTTCACCATTTTGGATAA
TAAGATATGGTTTCAGAAGTTTTATATCACAGAAGAAGGTGTTGCTCTTATAGAAATAGGACCTTGTTTTGTCTTAAATC
TCATAAACATTATTCAGGGAAGTTTTGGAGGACCAACTTTATATAAAAATTCTCTCTACCAGGCACCAAAAATGCATTGC
CATGTCATAAGATCCATCACACCTGCAAAATACAGAGAGAATCAGCAAGCGAAAGTTGTGCAGAAACTGAGAAAGAAAGA
GCCAAAGATCCTTCTTCCACATGAT

Alignment

ORF - retro_ggor_2657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.34 %
• Parental protein coverage: 85.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAATKRKRRGGFAVQAKKPKRNEKDAEPPAKRHATAEEVEEEERNRIPG-PVCKGKWKNKERILIFSSRG
          MAATKRK..GG.AVQAK.P.R.EK.AE.PAK..ATA.EVEEE.R..IPG.P...G..K.......F....
Retrocopy MAATKRKQHGGVAVQAKNPERSEKEAEQPAKLGATAKEVEEEDRDWIPG>PFARGSEKTRNGFSSFLPEE

Parental  -INFRTRHLMQDLRMLMPHSKADTKMDRKDKLFVINEVCEMKNCNKCIYFEAKKK-QDLYMWLSNSPHGP
          .INFRTRH.MQDLRMLMPHSKAD.KMDRK.K.F.I.E.CEMKNCNKCIYFEAKKK.QDL.M.LSNSPHGP
Retrocopy *INFRTRHFMQDLRMLMPHSKADAKMDRKHK*FEISEFCEMKNCNKCIYFEAKKK>QDLFM*LSNSPHGP

Parental  SAKFLVQNIHTLAELKMTGNCLKGSRPLLSFDPAFDELPHYALLKELLIQIFSTPRYHPKSQPFVDHVFT
          SAKFLVQN.H.LAELKMTGN.LKGS.P....DPAFDEL.HYALLKELLIQIFSTP.YHPKSQPFV..V.T
Retrocopy SAKFLVQNSHSLAELKMTGNLLKGSCPFC-LDPAFDELLHYALLKELLIQIFSTPWYHPKSQPFVGRVLT

Parental  FTILDNRIWFRNFQIIEEDAALVEIGPRFVLNLIKIFQGSFGGPTLYENPHYQSPNMHRRVIRSITAAKY
          FTILDN.IWF..F.I.EE..AL.EIGP.FVLNLI.I.QGSFGGPTLY.N..YQ.P.MH..VIRSIT.AKY
Retrocopy FTILDNKIWFQKFYITEEGVALIEIGPCFVLNLINIIQGSFGGPTLYKNSLYQAPKMHCHVIRSITPAKY

Parental  REKQQVKDVQKLRKKEPKTLLPHD
          RE.QQ.K.VQKLRKKEPK.LLPHD
Retrocopy RENQQAKVVQKLRKKEPKILLPHD

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	6.14 RPM
SRP007412_cerebellum	0.00 RPM	6.54 RPM
SRP007412_heart	0.09 RPM	1.19 RPM
SRP007412_kidney	0.00 RPM	7.81 RPM
SRP007412_liver	0.00 RPM	6.38 RPM
SRP007412_testis	0.00 RPM	14.09 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_2657 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2657 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3954
Pan troglodytes	retro_ptro_2684
Pongo abelii	retro_pabe_3258

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001790	2 retrocopies	retro_chof_1664, retro_chof_1776,
Callithrix jacchus	ENSCJAG00000018506	1 retrocopy	retro_cjac_1389,
Homo sapiens	ENSG00000113460	1 retrocopy	retro_hsap_3954,
Gorilla gorilla	ENSGGOG00000004225	1 retrocopy	retro_ggor_2657 ,
Loxodonta africana	ENSLAFG00000007249	1 retrocopy	retro_lafr_1116,
Myotis lucifugus	ENSMLUG00000029255	3 retrocopies	retro_mluc_1402, retro_mluc_707, retro_mluc_963,
Macaca mulatta	ENSMMUG00000000442	1 retrocopy	retro_mmul_2289,
Monodelphis domestica	ENSMODG00000020386	1 retrocopy	retro_mdom_1032,
Nomascus leucogenys	ENSNLEG00000014452	1 retrocopy	retro_nleu_533,
Otolemur garnettii	ENSOGAG00000014827	2 retrocopies	retro_ogar_3116, retro_ogar_793,
Pongo abelii	ENSPPYG00000015390	2 retrocopies	retro_pabe_3258, retro_pabe_3379,
Pan troglodytes	ENSPTRG00000016784	1 retrocopy	retro_ptro_2684,
Rattus norvegicus	ENSRNOG00000018021	1 retrocopy	retro_rnor_1140,
Tupaia belangeri	ENSTBEG00000011652	9 retrocopies	retro_tbel_1963, retro_tbel_1964, retro_tbel_2981, retro_tbel_3002, retro_tbel_3082, retro_tbel_4194, retro_tbel_4229, retro_tbel_4418, retro_tbel_954,