RetrogeneDB ID: retro_pabe_2464

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:120464695..120465319(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPF2
• Ensembl ID: ENSPPYG00000016925
• Aliases: None
• Description: ribosome production factor 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20870]

Sequence

>retro_pabe_2464
TCGAAATAGTCAGATTGTTCTTTATTCACGTATGGCTCCCATAAGAAGAAATGAACAAATAATCTAATAAGAGATCACAT
GTATGGCTATCTTTTGCTAGATATGATAGAATTAGGCATTGAGAAATTTGTCTCATTAATAGACATTAAGAACAGTAAAT
GCCCTGAGAAAACAAAACCCATGATAATATTTGCTGGTGAGGATTTTGATGTAAAAGAAGACTCTATAAGGCTAAAGAGT
CTTCTTACTGATTTTTTCAGCAGCCCAGGAGTATCAGATAGCCTCCCAACTGGATTAGAGTATGTTTTACACTTCACCAC
ACAGTAAGGGAAGATTTATTTTCGAAGTTATGAGTTACTGCTGAAGAAATCTGTAGCAGAATACCACAGATTGAAGTGGA
GATATGGAAACCTCATTGGATCGGGTTCTGAGGAGGACATACCTGGCATCAGATGAACTTTATAAATTATCTATGCAAAT
GCCAAAACTTTCAAGCCAAAGAGGAAGAAAATTATCTCCCATGATACTTTTGGTATAATTTGTGGAAGGATTCATATGCA
GAAGTAAGGCCTAAGCAAACTACAAACTGGGAAAATGAGGGGTTTGATGTAAACCCCTGAAGAA

Alignment

ORF - retro_pabe_2464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.81 %
• Parental protein coverage: 68.3 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SKKSDCSLFMFGSHNKKRPNNLVIGRMYDYHVLDMIELGIENFVSLKDIKNSKCPEGTKPMLIFAGDDFD
          SK.SDCSLF..GSH.KK..NNL....MY.Y..LDMIELGIE.FVSL.DIKNSKCPE.TKPM.IFAG.DFD
Retrocopy SK*SDCSLFTYGSHKKK*TNNLIRDHMYGYLLLDMIELGIEKFVSLIDIKNSKCPEKTKPMIIFAGEDFD

Parental  VTEDYRRLKSLLIDFFRGPTVSNIRLAGLEYVLHFTALNGKIYFRSYKLLLKKSGC-RTPRIELE-EMGP
          V.ED..RLKSLL.DFF..P.VS.....GLEYVLHFT...GKIYFRSY.LLLKKS...R.P.IE.E..M..
Retrocopy VKEDSIRLKSLLTDFFSSPGVSDSLPTGLEYVLHFTTQ*GKIYFRSYELLLKKSVA<RIPQIEVE<DMET

Parental  SLDLVLRRTHLASDDLYKLSMKMP-KALKPKKKKNISHDTFGTTYGRIHMQKQDLSKLQTRKMKGLKKRP
          SLD.VLRRT.LASD.LYKLSM.MP.K..KPK.KK.ISHDTFG...GRIHMQK..LSKLQT.KM.GL...P
Retrocopy SLDRVLRRTYLASDELYKLSMQMP<KTFKPKRKKIISHDTFGIICGRIHMQK*GLSKLQTGKMRGLM*TP

Parental  AE
          .E
Retrocopy EE

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	15.92 RPM
SRP007412_cerebellum	0.00 RPM	20.92 RPM
SRP007412_heart	0.00 RPM	9.63 RPM
SRP007412_kidney	0.00 RPM	11.83 RPM
SRP007412_liver	0.00 RPM	14.32 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2464 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2464 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2464 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1903
Callithrix jacchus	retro_cjac_2244

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003918	2 retrocopies	retro_cfam_1611, retro_cfam_903,
Callithrix jacchus	ENSCJAG00000005212	6 retrocopies	retro_cjac_1675, retro_cjac_1768, retro_cjac_2244, retro_cjac_2473, retro_cjac_606, retro_cjac_933,
Cavia porcellus	ENSCPOG00000006797	2 retrocopies	retro_cpor_332, retro_cpor_582,
Equus caballus	ENSECAG00000017121	1 retrocopy	retro_ecab_782,
Erinaceus europaeus	ENSEEUG00000006169	2 retrocopies	retro_eeur_454, retro_eeur_584,
Felis catus	ENSFCAG00000001527	1 retrocopy	retro_fcat_1584,
Homo sapiens	ENSG00000197498	1 retrocopy	retro_hsap_2425,
Gorilla gorilla	ENSGGOG00000001469	1 retrocopy	retro_ggor_83,
Myotis lucifugus	ENSMLUG00000005676	2 retrocopies	retro_mluc_485, retro_mluc_921,
Macaca mulatta	ENSMMUG00000021532	1 retrocopy	retro_mmul_1903,
Mus musculus	ENSMUSG00000038510	1 retrocopy	retro_mmus_2234,
Nomascus leucogenys	ENSNLEG00000012854	3 retrocopies	retro_nleu_2024, retro_nleu_2434, retro_nleu_2445,
Oryctolagus cuniculus	ENSOCUG00000016028	1 retrocopy	retro_ocun_831,
Pongo abelii	ENSPPYG00000016925	2 retrocopies	retro_pabe_1788, retro_pabe_2464 ,
Pan troglodytes	ENSPTRG00000018503	1 retrocopy	retro_ptro_1398,
Rattus norvegicus	ENSRNOG00000000587	1 retrocopy	retro_rnor_2336,
Tupaia belangeri	ENSTBEG00000017151	9 retrocopies	retro_tbel_1824, retro_tbel_2243, retro_tbel_2376, retro_tbel_2576, retro_tbel_3547, retro_tbel_3635, retro_tbel_3803, retro_tbel_3876, retro_tbel_4509,