RetrogeneDB ID: retro_pabe_3379

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8_random:13240094..13240993(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRIX1
• Ensembl ID: ENSPPYG00000015390
• Aliases: BRIX1, BRIX, BXDC2
• Description: ribosome biogenesis protein BRX1 homolog [Source:RefSeq peptide;Acc:NP_001125690]

Sequence

>retro_pabe_3379
ATGGCAGCAACCAAGAGGAAACAGCATGGAGGCTGGCAGTTCAGGCGAAGAACCCAGAAAGAAGTGAAAAAGAGGCCGAG
CAGCCAGCTAAGTTGGGCGCCACCACAGAGGAGGTGGAAGAAGAAGATGGAGACTGGATTCCAGGCCCTGTTTGCAAGGG
AGAGTGAAAAAACAAGGAATGTCATCTTTTCTTCCAGAGGAATAAATAAATTTCAGAACAAGGCATTTTATGCAGGACTT
GAGAATGTTGATGCCTCATTCTAAAGCAGATACTAAAATGGATAGTAAGCATAAATAATTTGAGATTAGCCAGTTCTGTG
AAATGAAAAACTGTAATAAATGCATCTACTTTGAAGCTAAGAAAAAAACAGGATCTCTTTATGTAGTTTTCAAATTCACT
TCATGGACCATCTGCTAAAGTCCTTGTTCAAAATATTCATACCCTAGCTGAACTAAAGATGACTGGAAACCTTTTGAAAG
GTTCTTGCCCCTTTTGTCTTGACCCAGCTTTTGATGAATTACTACATTCTGCTTTGTTAAAAGAACTCTTAATTCAGATC
TTTAGTACACCGTGGTATCATCCCAAAAGCCAACCATTCATGGGCCATGTGTTTACTTTCACCATTTTGAATAATAGGAT
ATGGTTTCAGAAGTTTCATATCATAGAAGAAGGTGTTGCTCTTGTAGAAATAGGACCTTGTTTTGTCTTAAATCTCATAA
ACATTATTCAGGGAAGTTTTGGAGGACCAACTTTATATGAAAATTCTCACTACCAGGCGCCAAAAATGCATTGCCATGTC
ATAAGATCCATCACACCTGCAAAATACAGAGAGAATCAGCAAGTGAAAGATGTGCGGAAACTGAGAAAGAAAGAGCCACA
GATCCTTCTTCCACATGAT

Alignment

ORF - retro_pabe_3379 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: 3

Retrocopy - Parental Gene Alignment:

Parental  MAATKRKRRGGF-AVQAKKPKRNEKDAEPPAKRHATAEEVEEEERDRIPGPVCKGKWKNKERILIFSSRG
          MAATKRK..GG..AVQAK.P.R.EK.AE.PAK..AT.EEVEEE..D.IPGPVCKG..KNKE..L.F....
Retrocopy MAATKRKQHGGW<AVQAKNPERSEKEAEQPAKLGATTEEVEEEDGDWIPGPVCKGE*KNKECHLFFQRNK

Parental  -INFRTRHLMQDLRMLMPHSKAASSLPWVEYLRGTLKVCEMKNCNKCIYFEAKKK-QDLYMWLSNSPHGP
          .INFRTRH.MQDLRMLMPHSKA................CEMKNCNKCIYFEAKKK.QDL.M..SNS.HGP
Retrocopy <INFRTRHFMQDLRMLMPHSKADTKMDSKHK*FEISQFCEMKNCNKCIYFEAKKK>QDLFM*FSNSLHGP

Parental  SAKFLVQNIHTLAELKMTGNCLKGSRPLLSFDPAFDELPHYALLKELLIQIFSTPRYHPKSQPFVDHVFT
          SAK.LVQNIHTLAELKMTGN.LKGS.P....DPAFDEL.H.ALLKELLIQIFSTP.YHPKSQPF..HVFT
Retrocopy SAKVLVQNIHTLAELKMTGNLLKGSCPFC-LDPAFDELLHSALLKELLIQIFSTPWYHPKSQPFMGHVFT

Parental  FTILDNRIWFRNFQIIEEDAALVEIGPRFVLNLIKIFQGSFGGPTLYENPHYQSPNMHRRVIRSITAAKY
          FTIL.NRIWF..F.IIEE..ALVEIGP.FVLNLI.I.QGSFGGPTLYEN.HYQ.P.MH..VIRSIT.AKY
Retrocopy FTILNNRIWFQKFHIIEEGVALVEIGPCFVLNLINIIQGSFGGPTLYENSHYQAPKMHCHVIRSITPAKY

Parental  REKQQVKDVQKLRKKEPKTLLPHD
          RE.QQVKDV.KLRKKEP..LLPHD
Retrocopy RENQQVKDVRKLRKKEPQILLPHD

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	6.91 RPM
SRP007412_cerebellum	0.00 RPM	15.81 RPM
SRP007412_heart	0.00 RPM	5.36 RPM
SRP007412_kidney	0.00 RPM	8.42 RPM
SRP007412_liver	0.00 RPM	8.23 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3379 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3379 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3379 has 0 orthologous retrocopies within eutheria group .

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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,