RetrogeneDB ID: retro_pabe_1810

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:20312558..20313530(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPAL1
• Ensembl ID: ENSPPYG00000014714
• Aliases: NIPAL1, NPAL1
• Description: magnesium transporter NIPA3 [Source:RefSeq peptide;Acc:NP_001125102]

Sequence

>retro_pabe_1810
GGCTCCAGCTTCATATTGAAAAAGAAGGGTCTCTTGCAACTGGCCAACAAAAGCATCATTAGAACTGGACAAGGTGGACA
TTCTGACCCGAAGGATGGCTCTGGGGGGCAGGAGTGCTGGCCATGGGAGCAGGAGAGGCTGCACATTTTGCTGCTTATGC
TTTTGCACCTGCCATCTTGGTCACCCTCACCCCCCCAGCCCTCTGAGTGTTCTCATAAGTGCAATATTATCTTCCTATTT
TTTAAATGAGCACTTGAACATTTATGGGAAAACAGGCTGCATATTGGGGTCAACTGTGATGGTTATCCATACCCCAGAAG
AAGAGGAAGTCACTTCTTTGCACGAAATGGAAATGAAATTGAGAGACCCAGGATTTATTTCCTTTGCTGTGATCATAATT
GTGATCTTGGTGTTGATTATGATTGTGGCTCCCAAGAAAGGACAGACCAATATATTGGTCTATGTTTCAATCTGTTGTTT
GACTGGAGCATTTTCAGTTTCTCATGCCAAAGGCCTGGGTATTGCCATTAAGGAATTACTAGAATGGAAGCCAGTTTAGA
AGCATGCCCTGGTCATTGTTTTGCTGGCTATACTTGTGTTTTTGGTGACTACACAGATTAACTATCTCAAGGCACCAGAC
ACCGTTAATACATCTCCTGTGACTCCCATTTATTTTGCGTTCTTCACATCCATGGTAGTGACTTGCTCTGCCATCTTACT
CCAAGAGTGGTATGGCATGAAAGCTGGAGATATCATCGAGACCCTGAATGGATTCTTCACTATTATCCTTGGCATCTTTC
TTCTACATGCTTTTAAAAATACTGACATTACCTGGAGTAAGCTGACATCCACTGCTAAGAAAGAAGTCATCTCTCTGAAT
GGCAATGAGAGCAGTCCTGTTTTACTAGAGAACTTGGAGTGTTTAGCCCTGGATACAATGATAACATTACCTTGTTTAGC
AGAACTGATGAT

Alignment

ORF - retro_pabe_1810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.38 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSSFILKKKGLLQLASKGITRAGQGGHSYLKE-WLWWVGLLSMGAGEAANFA--AYAFAPATLVTPLGA-
          GSSFILKKKGLLQLA.K.I.R.GQGGHS..K..WLW..G.L.MGAGEAA.FA..A.A.A.....TP....
Retrocopy GSSFILKKKGLLQLANKSIIRTGQGGHSDPKD<WLWGAGVLAMGAGEAAHFAAYAFAPAILVTLTPPAL<

Parental  LSVLISAILSSYFLNEHLNIHGKIGCILSILGSTVMVIHAPQEEEVTSLHEMEMKLRDPGFISFAVIVTV
          LSVLISAILSSYFLNEHLNI.GK.GC...ILGSTVMVIH.P.EEEVTSLHEMEMKLRDPGFISFAVI..V
Retrocopy LSVLISAILSSYFLNEHLNIYGKTGC---ILGSTVMVIHTPEEEEVTSLHEMEMKLRDPGFISFAVIIIV

Parental  ISLVLILIVAPKKGQTNILVYISICSLIGAFSVSSVKGLGIAIKELIEWKPVYKHPLVFVLLAVLVLSVT
          I.LVLI.IVAPKKGQTNILVY.SIC.L.GAFSVS..KGLGIAIKEL.EWKPV.KH.LV.VLLA.LV..VT
Retrocopy I-LVLIMIVAPKKGQTNILVYVSICCLTGAFSVSHAKGLGIAIKELLEWKPV*KHALVIVLLAILVFLVT

Parental  TQINYLNKALDTFNTSIVTPIYYVFFTSMVVTCSAILFQEWYGMTAGDIIGTLSGFFTIIIGIFLLHAFK
          TQINYL.KA.DT.NTS.VTPIY..FFTSMVVTCSAIL.QEWYGM.AGDII.TL.GFFTII.GIFLLHAFK
Retrocopy TQINYL-KAPDTVNTSPVTPIYFAFFTSMVVTCSAILLQEWYGMKAGDIIETLNGFFTIILGIFLLHAFK

Parental  NTDITWSELTSTAKKEAVSLNVSENNYVLLENLECSA-PGYNDDVTLFSRTDD
          NTDITWS.LTSTAKKE..SLN..E...VLLENLEC.A.PGYND..TLFSRTDD
Retrocopy NTDITWSKLTSTAKKEVISLNGNESSPVLLENLECLA<PGYNDNITLFSRTDD

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	0.11 RPM	0.17 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.21 RPM
SRP007412_kidney	0.00 RPM	2.55 RPM
SRP007412_liver	0.00 RPM	3.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1810 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1810 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1810 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002047	1 retrocopy	retro_dnov_2048,
Homo sapiens	ENSG00000163293	1 retrocopy	retro_hsap_2463,
Gorilla gorilla	ENSGGOG00000009006	1 retrocopy	retro_ggor_1533,
Macaca mulatta	ENSMMUG00000018625	1 retrocopy	retro_mmul_638,
Nomascus leucogenys	ENSNLEG00000017377	1 retrocopy	retro_nleu_2814,
Pongo abelii	ENSPPYG00000014714	1 retrocopy	retro_pabe_1810 ,
Pan troglodytes	ENSPTRG00000016038	1 retrocopy	retro_ptro_1422,