RetrogeneDB ID: retro_ptro_743

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:18690119..18690455(-)
• Located in intron of: ENSPTRG00000004741

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDFIP1
• Ensembl ID: ENSPTRG00000017358
• Aliases: None
• Description: None

Sequence

>retro_ptro_743
ATGGAGTTGGCATTAGTGGCACCAGTGGCAGTTGAGCTGGTCTGCAGCAGCAAGTACCAACATTTATAGAATGAGGAAGA
GCCTGAGGAACCTGAGAAGGCTTCAGGTGAGGTTCCTCCACCTTATAGCATCAACTCTGCAGAGAGTATGGTATATTTGA
CTACACAGATGAGTCTAATTTTCCAAAGCCCCCATTTTACAATGTGGTTGCAAACATTACCAATTTATAATAAAGTCATG
AGAATCAAGGCTGAAGCTCTTTCTTTGGTTCCTGGAAGAGATGAGGATTTTGTGGGACAGGATGATTTTGATGATGCTGA
CCAGCTGAGGATGGGA

Alignment

ORF - retro_ptro_743 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.96 %
• Parental protein coverage: 51.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALALAALAAVEPACGSRYQQLQNEEESGEPEQAAGDAPPPYSSISAESTAY-FDYKDESGFPKPPSYNV
          M.LAL.A..AVE..C.S.YQ.L.NEEE..EPE.A.G..PPPYS..SAES..Y.FDY.DES.FPKPP.YNV
Retrocopy MELALVAPVAVELVCSSKYQHL*NEEEPEEPEKASGEVPPPYSINSAESMVY<FDYTDESNFPKPPFYNV

Parental  AT-TLPSYDEAERTKAEATIPLVPGRDEDFVGRDDFDDADQLRIG
          ...TLP.Y....R.KAEA...LVPGRDEDFVG.DDFDDADQLR.G
Retrocopy VA>TLPIYNKVMRIKAEA-LSLVPGRDEDFVGQDDFDDADQLRMG

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	247.67 RPM
SRP007412_cerebellum	0.00 RPM	165.55 RPM
SRP007412_heart	0.00 RPM	70.83 RPM
SRP007412_kidney	0.00 RPM	119.88 RPM
SRP007412_liver	0.03 RPM	68.81 RPM
SRP007412_testis	0.00 RPM	92.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_743 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_743 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_743 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1091
Gorilla gorilla	retro_ggor_859
Pongo abelii	retro_pabe_908
Macaca mulatta	retro_mmul_846
Callithrix jacchus	retro_cjac_3175

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047747	1 retrocopy	retro_btau_766,
Callithrix jacchus	ENSCJAG00000018271	1 retrocopy	retro_cjac_3175,
Equus caballus	ENSECAG00000021907	1 retrocopy	retro_ecab_261,
Homo sapiens	ENSG00000131507	1 retrocopy	retro_hsap_1091,
Gorilla gorilla	ENSGGOG00000004879	1 retrocopy	retro_ggor_859,
Macaca mulatta	ENSMMUG00000016787	1 retrocopy	retro_mmul_846,
Pongo abelii	ENSPPYG00000015896	1 retrocopy	retro_pabe_908,
Pan troglodytes	ENSPTRG00000017358	1 retrocopy	retro_ptro_743 ,
Sarcophilus harrisii	ENSSHAG00000002466	1 retrocopy	retro_shar_738,
Sus scrofa	ENSSSCG00000025295	1 retrocopy	retro_sscr_301,
Ictidomys tridecemlineatus	ENSSTOG00000005153	1 retrocopy	retro_itri_1454,