RetrogeneDB ID: retro_pabe_908

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:19075909..19076239(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDFIP1
• Ensembl ID: ENSPPYG00000015896
• Aliases: None
• Description: Nedd4 family interacting protein 1 [Source:HGNC Symbol;Acc:17592]

Sequence

>retro_pabe_908
TTGGCATTAGTGGCACCAGTGGCAGTTGAGCTGGTCTGCAGCAGCAAGTACCAACATTTATAGGATGAGGAAGAGCCTGA
GGAACCTGAGAAGGCTTCAGGTGAGGTTCCTCCACCTTATGGCGTCAACTCTGCAGAGAGTATGGTATATTTGACTACAC
AGATGAGTCTAATTTTCCAAAGCCCCCATTTTACAATGTGGTTGCAAACATTACCAATTTATAATAAAGTCATGAGAATC
AAGGCTGAAGCTCTTTCTTTGGTTCCTGGAAGAGATGAGGATTTTGTGGGACAGGATGATTTTGATGATGCTGACCAGTT
GAGGATAGGA

Alignment

ORF - retro_pabe_908 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.37 %
• Parental protein coverage: 50.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LALAALAAVEPACGSRYQQLQNEEESGEPEQAAGDAPPPYSSISAESAAY-FDYKDESGFPKPPSYNVAT
          LAL.A..AVE..C.S.YQ.L..EEE..EPE.A.G..PPPY...SAES..Y.FDY.DES.FPKPP.YNV..
Retrocopy LALVAPVAVELVCSSKYQHL*DEEEPEEPEKASGEVPPPYGVNSAESMVY<FDYTDESNFPKPPFYNVVA

Parental  -TLPSYDEAERTKAEATIPLVPGRDEDFVGRDDFDDADQLRIG
          .TLP.Y....R.KAEA...LVPGRDEDFVG.DDFDDADQLRIG
Retrocopy >TLPIYNKVMRIKAEA-LSLVPGRDEDFVGQDDFDDADQLRIG

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	236.87 RPM
SRP007412_cerebellum	0.00 RPM	179.60 RPM
SRP007412_heart	0.00 RPM	40.16 RPM
SRP007412_kidney	0.00 RPM	94.07 RPM
SRP007412_liver	0.00 RPM	66.34 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_908 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_908 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_908 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1091
Pan troglodytes	retro_ptro_743
Gorilla gorilla	retro_ggor_859
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,