RetrogeneDB ID: retro_pabe_3195

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:155367534..155368200(-)
• Located in intron of: ENSPPYG00000018227

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBXN2B
• Ensembl ID: ENSPPYG00000018610
• Aliases: None
• Description: UBX domain protein 2B [Source:HGNC Symbol;Acc:27035]

Sequence

>retro_pabe_3195
GACACCACCTCAACGTCATTTACAGGTGGAGGATACAGATTGGGTAATTCCTTTTGTAAGCGGTCTGAATATATGCATGG
AGAAAATCAGCTGCAAGATGTTCAGATTTTGCTTAAACTGTGGAGCAATGGTTTCAGTTTAGATGATCGAGAATTGAGAC
CTTACAATGAACCAACAAATGCTCAATTTCTGGAGTCTGTTAAGAGAGGAGAGATCCCCCGGGAGCTTCAGTGCCTTGTT
CATGGTGGCCAAGTGATTTGGGATATGGAGGACCATCAGGATCAAGAATACATAAAACCTAGATTGAGGTTCAAGGCTTT
TAGTAGGGAAGGGCAAAAACTTGGAAGGCTTACACCTGAAATAGTCAGTACACCTTCTTCTCCAGAAGAGGAGGATAAAT
CAATACTTAACACGGTTGTTCTTACTGATGATTCAGTGCCAACAACAAAAATTCAAATCAGGTTAGCAGATGGGAGTCGT
TTGACACAAAGATTCAATAGTACACACAGGATCCTGGATGTCCGGAACTTTATTGTACAGTCTCGTCCTGAATTTGCAGC
TCTTGACTTTATTCTTGTGACTTCATTTCCGAATAAAGAGCTAACAGATGAAAGCCTGACACTGCTAGAAGCAGATATTC
TTAACACTGTGTTACTCCATCAACTA

Alignment

ORF - retro_pabe_3195 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.34 %
• Parental protein coverage: 67.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDKSKSFTGGGYRLGSSFCKRSEYIYGENQLQDVQILLKLWSNGFSLDDGELRPYNEPTNAQFLESVKRG
          D..S.SFTGGGYRLG.SFCKRSEY..GENQLQDVQILLKLWSNGFSLDD.ELRPYNEPTNAQFLESVKRG
Retrocopy DTTSTSFTGGGYRLGNSFCKRSEYMHGENQLQDVQILLKLWSNGFSLDDRELRPYNEPTNAQFLESVKRG

Parental  EIPLELQRLVHGGQVNLDMEDHQDQEYIKPRLRFKAFSGEGQKLGSLTPEIVSTPSSPEEEDKSILNAVV
          EIP.ELQ.LVHGGQV..DMEDHQDQEYIKPRLRFKAFS.EGQKLG.LTPEIVSTPSSPEEEDKSILN.VV
Retrocopy EIPRELQCLVHGGQVIWDMEDHQDQEYIKPRLRFKAFSREGQKLGRLTPEIVSTPSSPEEEDKSILNTVV

Parental  LIDDSVPTTKIQIRLADGSRLIQRFNSTHRILDVRNFIVQSRPEFAALDFILVTSFPNKELTDESLTLLE
          L.DDSVPTTKIQIRLADGSRL.QRFNSTHRILDVRNFIVQSRPEFAALDFILVTSFPNKELTDESLTLLE
Retrocopy LTDDSVPTTKIQIRLADGSRLTQRFNSTHRILDVRNFIVQSRPEFAALDFILVTSFPNKELTDESLTLLE

Parental  ADILNTVLLQQL
          ADILNTVLL.QL
Retrocopy ADILNTVLLHQL

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	5.31 RPM
SRP007412_cerebellum	0.12 RPM	9.00 RPM
SRP007412_heart	0.03 RPM	1.96 RPM
SRP007412_kidney	0.03 RPM	3.25 RPM
SRP007412_liver	0.03 RPM	2.48 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3195 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3195 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3195 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3923
Pan troglodytes	retro_ptro_2668

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000215114	1 retrocopy	retro_hsap_3923,
Nomascus leucogenys	ENSNLEG00000001356	1 retrocopy	retro_nleu_2984,
Pongo abelii	ENSPPYG00000010851	1 retrocopy	retro_pabe_3324,
Pongo abelii	ENSPPYG00000018610	1 retrocopy	retro_pabe_3195 ,
Pan troglodytes	ENSPTRG00000033886	1 retrocopy	retro_ptro_2668,