RetrogeneDB ID: retro_ptro_2684

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:49120011..49120757(+)
• Located in intron of: ENSPTRG00000020241

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRIX1
• Ensembl ID: ENSPTRG00000016784
• Aliases: BRIX1, BRIX, BXDC2
• Description: BRX1, biogenesis of ribosomes, homolog [Source:UniProtKB/TrEMBL;Acc:K7BDK1]

Sequence

>retro_ptro_2684
GGGGAGTGAAAAAACAAGGAATGGATTTTCATCTTTTCTTCCAGAGGAATAAATAAATTTCAGAACAAGACATTTTATGC
AGGACTTGAGAATGTTGATGCCTCATTCTAAAGCAGATGCTAAAATGGATCGTAAGCATAAATAATTTGAGATTAGTGAG
TTCTGTGAAATGAAAAACTGTAATAAATGCATCTACTTTGAAGCTAAGAAAAAAACAGGATCTCTTTATGTAGCTTTCAA
ATTCACCTCATGGACCATCTGCTAAATTCCCTGTTCAAAATAGTCATAGCCTAGCTGAACTACAGATGACTGGAAACCTT
TTGAAAGGTTCTTGCCCCTTTTGTCTTGACCCAGCTTTTGATGAATTACTACATTATGCTTTGTTAAAAGAACTCTTAAT
TCAGATCTTTAGTACACCGTGGTATCATCCCAAAAGCCAACCATTCGTGGGCCATGTGTTGACTTTCACCATTTTGGATA
ATACGATATGGTTTCAGAAGTTTTATATCATAGAAGAAGGTGTTGCTCTTGTAGAAATAGGACCTTGTTTTGTCTTAAAT
CTCATAAACATTATTCAGGGAAGTTTTGGAGGACCAACTTTATATAAAAATTCTCACTACCAGGCACCAAAAATGCATTG
CCATGTCATAAGATCCATCACACCTGCAAAATACAGAGAGAATCAGCAAGCGAAAGATGTGCAGAAACTGAGAAAGAAAG
AGCCAAAGATCCTTCTTCCATGTGAT

Alignment

ORF - retro_ptro_2684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.88 %
• Parental protein coverage: 82.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKWKNKERILIFSSRGIN-FRTR-HLMQDLRMLMPHSKADTKMDRKDKLFVINEVCEMKNCNKCIYFEAK
          G..KNKE.I.IFSSRGIN.F....H.MQDLRMLMPHSKAD.KMDRK.K.F.I.E.CEMKNCNKCIYFEAK
Retrocopy GE*KNKEWIFIFSSRGINKFQNK>HFMQDLRMLMPHSKADAKMDRKHK*FEISEFCEMKNCNKCIYFEAK

Parental  -KKQDLYMWLSNSPHGPSAKFLVQNIHTLAELKMTGNCLKGSRPLLSFDPAFDELPHYALLKELLIQIFS
          .KKQDL.M.LSNSPHGPSAKF.VQN.H.LAEL.MTGN.LKGS.P....DPAFDEL.HYALLKELLIQIFS
Retrocopy >KKQDLFM*LSNSPHGPSAKFPVQNSHSLAELQMTGNLLKGSCP-FCLDPAFDELLHYALLKELLIQIFS

Parental  TPRYHPKSQPFVDHVFTFTILDNRIWFRNFQIIEEDAALVEIGPRFVLNLIKIFQGSFGGPTLYENPHYQ
          TP.YHPKSQPFV.HV.TFTILDN.IWF..F.IIEE..ALVEIGP.FVLNLI.I.QGSFGGPTLY.N.HYQ
Retrocopy TPWYHPKSQPFVGHVLTFTILDNTIWFQKFYIIEEGVALVEIGPCFVLNLINIIQGSFGGPTLYKNSHYQ

Parental  SPNMHRRVIRSITAAKYREKQQVKDVQKLRKKEPKTLLPHD
          .P.MH..VIRSIT.AKYRE.QQ.KDVQKLRKKEPK.LLP.D
Retrocopy APKMHCHVIRSITPAKYRENQQAKDVQKLRKKEPKILLPCD

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	0.04 RPM	6.04 RPM
SRP007412_cerebellum	0.00 RPM	6.06 RPM
SRP007412_heart	0.06 RPM	3.58 RPM
SRP007412_kidney	0.00 RPM	5.96 RPM
SRP007412_liver	0.00 RPM	5.24 RPM
SRP007412_testis	0.11 RPM	8.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2684 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2684 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2684 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3954
Gorilla gorilla	retro_ggor_2657
Pongo abelii	retro_pabe_3258

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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,