RetrogeneDB ID: retro_pabe_2329

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:107098630..107099089(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFU1
• Ensembl ID: ENSPPYG00000012339
• Aliases: None
• Description: NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16287]

Sequence

>retro_pabe_2329
TTTGAGACAAGGCCCATGGATTTTCCCACCCCAGCTGCAGCATTTCGCTCGCCTTTGGATAGGCAGTTATTTAGGATTGA
AGGAGTAAAAAGTGTTTTCTTTGGGCCAGATTTCATCACTGCCACAAAGGAAAATGAAAAATTAGACTGGAATTTACTGA
AACCAGATATTTACACAACAACCACGGACTTCTTTGCATCTGGTTTATCCCTAGTTACTGAGGAAACATCTTCAGGAGAA
GCAGGATGTGAAGATGATGAAGTTGTGGCATTGATTAAAGAAGTGTTAGATACTAGAATGTGGCCAACTGTGCAAGAAGA
TGGAGGAGATGTAATCTACAAAGGCTTTGAAGATGGTATCGTATGACTGAAACTCCAGGGTTCTTGTACCAGCTGCCCTA
GTTCAATCATTACTCTGAAAAATGGAATTCAGAACATGCTGCAGTTTTATATTCCAGAG

Alignment

ORF - retro_pabe_2329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.62 %
• Parental protein coverage: 74.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FVQRPL-FPLP-AAF---CNTQLFRVEGVKSVFFGPDFITVTKENEELDWNLLKPDIYATIMDFFASGLP
          F..RP..FP.P.AAF......QLFR.EGVKSVFFGPDFIT.TKENE.LDWNLLKPDIY.T..DFFASGL.
Retrocopy FETRPMDFPTPAAAFRSPLDRQLFRIEGVKSVFFGPDFITATKENEKLDWNLLKPDIYTTTTDFFASGLS

Parental  LVTEETPSGEAGSEEDDEVVAMIKELLDTRI-RTVQEDGGDVIYKGF-DGIVQL-LQGSCTSCPSSIITL
          LVTEET.SGEAG..EDDEVVA.IKE.LDTR...TVQEDGGDVIYKGF.DGIV.L.LQGSCTSCPSSIITL
Retrocopy LVTEETSSGEAGC-EDDEVVALIKEVLDTRMWPTVQEDGGDVIYKGFEDGIV*LKLQGSCTSCPSSIITL

Parental  -NGIQ-MLQFVMDD
          .NGIQ.MLQF....
Retrocopy KNGIQNMLQFYIPE

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	1.05 RPM	4.81 RPM
SRP007412_cerebellum	1.58 RPM	4.62 RPM
SRP007412_heart	3.58 RPM	12.61 RPM
SRP007412_kidney	3.71 RPM	13.09 RPM
SRP007412_liver	1.81 RPM	6.33 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2329 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2329 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2329 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2638
Pan troglodytes	retro_ptro_1778
Macaca mulatta	retro_mmul_1524

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005978	1 retrocopy	retro_chof_456,
Callithrix jacchus	ENSCJAG00000019156	1 retrocopy	retro_cjac_1573,
Echinops telfairi	ENSETEG00000019002	1 retrocopy	retro_etel_1371,
Homo sapiens	ENSG00000169599	1 retrocopy	retro_hsap_2638,
Macaca mulatta	ENSMMUG00000000435	1 retrocopy	retro_mmul_1524,
Monodelphis domestica	ENSMODG00000011805	1 retrocopy	retro_mdom_1395,
Mustela putorius furo	ENSMPUG00000006663	1 retrocopy	retro_mputfur_67,
Mus musculus	ENSMUSG00000029993	1 retrocopy	retro_mmus_1401,
Nomascus leucogenys	ENSNLEG00000010101	1 retrocopy	retro_nleu_646,
Ochotona princeps	ENSOPRG00000016760	2 retrocopies	retro_opri_380, retro_opri_48,
Pongo abelii	ENSPPYG00000012339	1 retrocopy	retro_pabe_2329 ,
Pan troglodytes	ENSPTRG00000012016	1 retrocopy	retro_ptro_1778,
Tupaia belangeri	ENSTBEG00000008616	1 retrocopy	retro_tbel_525,
Tarsius syrichta	ENSTSYG00000013765	1 retrocopy	retro_tsyr_108,