RetrogeneDB ID: retro_pabe_328

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:183219391..183219883(+)
• Located in intron of: ENSPPYG00000001391

Retrocopy information

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

Parental gene information

• Parental gene symbol: NENF
• Ensembl ID: ENSPPYG00000000236
• Aliases: None
• Description: neudesin neurotrophic factor [Source:HGNC Symbol;Acc:30384]

Sequence

>retro_pabe_328
CAGTTGCAGCTGTAGCCACTAGCAGGGTTGACCCTGGTCCTGGTGCAGCCCCCAGGGCTGCTTGCAGCTCTGGCCAGGCA
GGTGCCATGCCCTACTAAGCAGAAACCCCTGGTCTGCCTCTTTATTGAGGAGGAGGCGGCCCACTATGGAGAGAAGAAAA
ACAGCCCATCTGCATGACAGTGAAGGGAGTGGTGTTTTATATCACCTCCAGAAAGGAATTTTATGGAAGAAGGGGCCCCC
TATAATGCATTGACCAGGAAAGTCCACCAGAGGGATAGCCAAGATGTCCCTGGGTCCTCCAGACCTCACCCATGAAACTC
TGGGTCTCATGGCCAAAGAGCTGGAATCCCTGGTTGATATCTTCACCAAAGTGTACAAAACCAAATATCCCATGGTTAGC
TACACAGCCTGAAGAATTCTTAATAGGGACAGCACCCCAGCCTGGACTTCAAACCTGAAGACCAACCCCATTTTGACATA
AAGAATGTGTTC

Alignment

ORF - retro_pabe_328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.06 %
• Parental protein coverage: 96.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QRQLRPLAALALVLALAPGLPTTRAGQTPRPAERGPPVRLFTEEELARYGGE-EEDQPIYLAVKGVVFDV
          Q.QL.PLA.L.LVL...PGL....A.Q.P.P....P.V.LF.EEE.A.Y.GE.EE.QPI...VKGVVF..
Retrocopy QLQL*PLAGLTLVLVQPPGLLAALARQVPCPTKQKPLVCLFIEEEAAHY-GE<EEKQPICMTVKGVVFYI

Parental  TSGKEFYGR-GAPYNALT-GKDSTRGVAKMSLDPADLTHDTTGLTAKELEALDEVFTKVYKAKYPIVGYT
          TS.KEFYGR.GAPYNALT.GK.STRG.AKMSL.P.DLTH.T.GL.AKELE.L...FTKVYK.KYP.V.YT
Retrocopy TSRKEFYGR>GAPYNALT>GK-STRGIAKMSLGPPDLTHETLGLMAKELESLVDIFTKVYKTKYPMVSYT

Parental  ARRILNEDGS-PNLDFKPEDQPHFDIKDEF
          A.RILN.D...P.LDFKPEDQPHFDIK..F
Retrocopy A*RILNRDST<PSLDFKPEDQPHFDIKNVF

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	18.96 RPM
SRP007412_cerebellum	0.00 RPM	10.21 RPM
SRP007412_heart	0.00 RPM	11.23 RPM
SRP007412_kidney	0.00 RPM	23.37 RPM
SRP007412_liver	0.00 RPM	11.48 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_328 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_328 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_328 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_379
Pan troglodytes	retro_ptro_295
Macaca mulatta	retro_mmul_490
Bos taurus	retro_btau_1238

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001341	1 retrocopy	retro_amel_836,
Bos taurus	ENSBTAG00000000759	1 retrocopy	retro_btau_1238,
Dasypus novemcinctus	ENSDNOG00000003399	1 retrocopy	retro_dnov_1256,
Felis catus	ENSFCAG00000031796	1 retrocopy	retro_fcat_1171,
Homo sapiens	ENSG00000117691	2 retrocopies	retro_hsap_3288, retro_hsap_379,
Gorilla gorilla	ENSGGOG00000025197	1 retrocopy	retro_ggor_830,
Macaca mulatta	ENSMMUG00000002142	2 retrocopies	retro_mmul_2064, retro_mmul_490,
Mus musculus	ENSMUSG00000037499	1 retrocopy	retro_mmus_3309,
Nomascus leucogenys	ENSNLEG00000002893	1 retrocopy	retro_nleu_1354,
Ochotona princeps	ENSOPRG00000014204	2 retrocopies	retro_opri_127, retro_opri_775,
Pongo abelii	ENSPPYG00000000236	2 retrocopies	retro_pabe_2717, retro_pabe_328 ,
Pan troglodytes	ENSPTRG00000001961	2 retrocopies	retro_ptro_2224, retro_ptro_295,
Sus scrofa	ENSSSCG00000015597	1 retrocopy	retro_sscr_393,
Ictidomys tridecemlineatus	ENSSTOG00000022293	2 retrocopies	retro_itri_1876, retro_itri_340,
Tarsius syrichta	ENSTSYG00000001880	3 retrocopies	retro_tsyr_1189, retro_tsyr_411, retro_tsyr_549,