RetrogeneDB ID: retro_ptro_1778

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:40274297..40274955(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFU1
• Ensembl ID: ENSPTRG00000012016
• Aliases: None
• Description: None

Sequence

>retro_ptro_1778
CAGCCTCTGCATCAATTTGTAGAAAGACTACTCTTCCCACTACCTGCAGCCTTTTGTAACCCAGTGAGATACATGTTTAT
TCAAACACAAGATATCTCAAATCCTAACAGTTTAAAGTTTATACCATGAAAACCAGTTTTTGAGACAAGGCCCATGGATT
TTCCAACCCCAGCTGCAGCATTTCGCTCCCCTTTGGCTATGCAGTTATTTAGGATTGAAGGAGTAAAAAGTGTTTTCTTT
GGGCCAGATTTCATCACTGCCACAAAGGAAAATGAAAAATTAGACTGGAATTTACTGAAACCAGATATTTACGCAATAAC
CACGGACTTCTTTGCATCTGGTTTACCCCTAGTTACTGAGGAAACATCTTCAAGGAGAAGCAGGATGTGAAGATGATGAA
GTTGTGGCATTGATTAAGGAAGTGTTAGATACTAGAATGCGGCCAACTGTGCAAGAAGATGGAGGAGACGTAATCTACAA
AGGCTTTGAAGATGGTATCGTATGACTGAAACTCCAGGGTTCTTGTACCAGCTGCCCTAGTTCAATCATTACTCTGAAAA
ATGGAATTCAGAACATGCTGCAGTTTTATATTCCAGAGGTAGAAGGTGTAGAACAGGGTATGGATGATCAATCAGATGAA
AAGGAAGCAAACTCGCCT

Alignment

ORF - retro_ptro_1778 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.14 %
• Parental protein coverage: 86.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QPLHQFVQRPLFPLPAAFYNPVRYMFIQTQDTPNPNSLKFIPGKPVLETRTMDFPTPAAAFRSPLARQLF
          QPLHQFV.R.LFPLPAAF.NPVRYMFIQTQD..NPNSLKFIP.KPV.ETR.MDFPTPAAAFRSPLA.QLF
Retrocopy QPLHQFVERLLFPLPAAFCNPVRYMFIQTQDISNPNSLKFIP*KPVFETRPMDFPTPAAAFRSPLAMQLF

Parental  RIEGVKSVFFGPDFITVTKENEELDWNLLKPDIYATIMDFFASGLPLVTEETPS-GEAGSEEDDEVVAMI
          RIEGVKSVFFGPDFIT.TKENE.LDWNLLKPDIYA...DFFASGLPLVTEET.S.GEAG..EDDEVVA.I
Retrocopy RIEGVKSVFFGPDFITATKENEKLDWNLLKPDIYAITTDFFASGLPLVTEETSS>GEAGC-EDDEVVALI

Parental  KELLDTRIRPTVQEDGGDVIYKGFEDGIVQLKLQGSCTSCPSSIITLKNGIQNMLQFYIPEVEGVEQVMD
          KE.LDTR.RPTVQEDGGDVIYKGFEDGIV.LKLQGSCTSCPSSIITLKNGIQNMLQFYIPEVEGVEQ.MD
Retrocopy KEVLDTRMRPTVQEDGGDVIYKGFEDGIV*LKLQGSCTSCPSSIITLKNGIQNMLQFYIPEVEGVEQGMD

Parental  DESDEKEANSP
          D.SDEKEANSP
Retrocopy DQSDEKEANSP

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	17.41 RPM
SRP007412_cerebellum	0.00 RPM	16.78 RPM
SRP007412_heart	0.00 RPM	41.97 RPM
SRP007412_kidney	0.03 RPM	30.86 RPM
SRP007412_liver	0.00 RPM	13.03 RPM
SRP007412_testis	0.00 RPM	36.25 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1778 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1778 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1778 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2638
Pongo abelii	retro_pabe_2329
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,