RetrogeneDB ID: retro_pabe_2326

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:99092322..99092672(-)
• Located in intron of: ENSPPYG00000013917

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000007237
• Aliases: None
• Description: None

Sequence

>retro_pabe_2326
GCTCCTGTAGGGGTGCAAAAACAGCGTGGCCAGGCCGGGGTCTGAGCTGGGGTTCTGTCCCTGCTGGGCTACGGCCCCAG
CTGGACTGCTGCCACAGAACTCAGCGCCGAATAACTCCAGAAGAAGCTGCAGTGGGACCCAGAGGCGAAGCATATTGAGG
TGGAGGACGTGACCCTCAACCATTGTGCCTGCAGCTTCTGAGTCCTGGTGGTGTTGGCCAAGTTCAAGGGGAAGCTGCTG
CTTCAGACACACTGGTGGGTAAACATGTGCCTAGCTGGAGGCTCTCGCACATCCATACTTTTGAGCAGAAAACCCTCATC
CCAGAGCAGTGGGCCTGTGAATGGCAGAAA

Alignment

ORF - retro_pabe_2326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.56 %
• Parental protein coverage: 77.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEVAPVRQQGSAAAVRGVVSRLGCRPSWTTAMELSAEYLREKLQRDLEAEHVEVEDTTLNRCACSFRVLV
          A.V....Q.G.A....GV.S.LG..PSWT.A.ELSAE.L..KLQ.D.EA.H.EVED.TLN.CACSF.VLV
Retrocopy APVGVQKQRGQAGV*AGVLSLLGYGPSWTAATELSAE*LQKKLQWDPEAKHIEVEDVTLNHCACSF*VLV

Parental  VSAKFEGKPLLQRHRLVNACLAE-ELPHIHAFEQKTLTPEQWARQRQK
          V.AKF.GK.LLQ.H..VN.CLA...L.HIH.FEQKTL.PEQWA...QK
Retrocopy VLAKFKGKLLLQTHWWVNMCLAG<RLSHIHTFEQKTLIPEQWACEWQK

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	5.47 RPM
SRP007412_cerebellum	0.00 RPM	3.53 RPM
SRP007412_heart	0.00 RPM	3.49 RPM
SRP007412_kidney	0.00 RPM	8.49 RPM
SRP007412_liver	0.00 RPM	6.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2326 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2326 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2326 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_1327
Macaca mulatta	retro_mmul_1522

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006661	1 retrocopy	retro_cjac_1327,
Echinops telfairi	ENSETEG00000006548	1 retrocopy	retro_etel_457,
Homo sapiens	ENSG00000169627	1 retrocopy	retro_hsap_2644,
Gorilla gorilla	ENSGGOG00000012724	2 retrocopies	retro_ggor_1847, retro_ggor_75,
Loxodonta africana	ENSLAFG00000017910	1 retrocopy	retro_lafr_712,
Myotis lucifugus	ENSMLUG00000003449	1 retrocopy	retro_mluc_2380,
Macaca mulatta	ENSMMUG00000007331	3 retrocopies	retro_mmul_1344, retro_mmul_1522, retro_mmul_1752,
Monodelphis domestica	ENSMODG00000015658	1 retrocopy	retro_mdom_1704,
Nomascus leucogenys	ENSNLEG00000001018	2 retrocopies	retro_nleu_1222, retro_nleu_650,
Oryctolagus cuniculus	ENSOCUG00000007562	1 retrocopy	retro_ocun_241,
Ochotona princeps	ENSOPRG00000002109	2 retrocopies	retro_opri_243, retro_opri_492,
Pongo abelii	ENSPPYG00000007237	2 retrocopies	retro_pabe_1608, retro_pabe_2326 ,
Pan troglodytes	ENSPTRG00000007990	2 retrocopies	retro_ptro_1284, retro_ptro_1781,
Rattus norvegicus	ENSRNOG00000047988	2 retrocopies	retro_rnor_322, retro_rnor_379,
Sorex araneus	ENSSARG00000003579	2 retrocopies	retro_sara_106, retro_sara_278,
Tarsius syrichta	ENSTSYG00000006274	1 retrocopy	retro_tsyr_1321,
Tursiops truncatus	ENSTTRG00000005543	2 retrocopies	retro_ttru_127, retro_ttru_1700,