RetrogeneDB ID: retro_ptro_2668

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:158547902..158548568(-)
• Located in intron of: ENSPTRG00000019919

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBXN2B
• Ensembl ID: ENSPTRG00000033886
• Aliases: None
• Description: None

Sequence

>retro_ptro_2668
GACACCACCTCAACGTCATTTACAGGTGGAGGATACAGATTGGGTAATTCCTTTTGTAAGCGGTCTGAATATATGCATGG
AGAAAATCAGCTGCAAGATGTTCAGATTTTGCTTAAACTGTGGAGCAATGGTTTCAGTTTAGATGATGGAGAATTGAGAC
CTTACAATGAACCAACAAATGCTCAATTTCTGGAGTTTAAGATAGGAGAGATCCCCCTGGAGCTTCAGTGCCTTGTTCAT
GGGGGCCAAGTGAATTGGGATATGGAGGACCATCAGGATCAAGAATACATAAAACCTAGATTGAGGTTCAAGGCTTTTAG
TGGAGAAGGGCAAAAACTTGGAAGGCTTACACCTGAAATAGTCAGTGCACCTTCCTCTCCAGAAGAGGAGGATAAATCAA
TACTTAACGCGGTTGTTCTTATTGATGATTCAGTGCCAACAACAAAAATTCAAATCAGGTTAGCAGATGGGAGTCGTTTG
ATACAAAGATTCAATAGTACACACAGGATCCTGGATGTCCGGAACTTTATTGTACAGTCTTGTCCTGAATTTGCAGCTCT
TGACTTTATTCCTGTGACTTCATTTCCGAATAAAGAGCTAACAGATGAAAGCCTGACACTGCTAGAAGCAGATATTCTTA
ACACTGTGTTACTCCATCAACTAAAA

Alignment

ORF - retro_ptro_2668 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.83 %
• Parental protein coverage: 67.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDKSKSFTGGGYRLGSSFCKRSEYIYGENQLQDVQILLKLWSNGFSLDDGELRPYNEPTNAQFLESVKRG
          D..S.SFTGGGYRLG.SFCKRSEY..GENQLQDVQILLKLWSNGFSLDDGELRPYNEPTNAQFLE..K.G
Retrocopy DTTSTSFTGGGYRLGNSFCKRSEYMHGENQLQDVQILLKLWSNGFSLDDGELRPYNEPTNAQFLE-FKIG

Parental  EIPLELQRLVHGGQVNLDMEDHQDQEYIKPRLRFKAFSGEGQKLGSLTPEIVSTPSSPEEEDKSILNAVV
          EIPLELQ.LVHGGQVN.DMEDHQDQEYIKPRLRFKAFSGEGQKLG.LTPEIVS.PSSPEEEDKSILNAVV
Retrocopy EIPLELQCLVHGGQVNWDMEDHQDQEYIKPRLRFKAFSGEGQKLGRLTPEIVSAPSSPEEEDKSILNAVV

Parental  LIDDSVPTTKIQIRLADGSRLIQRFNSTHRILDVRNFIVQSRPEFAALDFILVTSFPNKELTDESLTLLE
          LIDDSVPTTKIQIRLADGSRLIQRFNSTHRILDVRNFIVQS.PEFAALDFI.VTSFPNKELTDESLTLLE
Retrocopy LIDDSVPTTKIQIRLADGSRLIQRFNSTHRILDVRNFIVQSCPEFAALDFIPVTSFPNKELTDESLTLLE

Parental  ADILNTVLLQQLK
          ADILNTVLL.QLK
Retrocopy ADILNTVLLHQLK

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	0.09 RPM	28.28 RPM
SRP007412_cerebellum	0.00 RPM	44.56 RPM
SRP007412_heart	0.06 RPM	11.78 RPM
SRP007412_kidney	0.08 RPM	23.56 RPM
SRP007412_liver	0.00 RPM	8.45 RPM
SRP007412_testis	0.11 RPM	25.82 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2668 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2668 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2668 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3923
Pongo abelii	retro_pabe_3195

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 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	ENSPPYG00000018610	1 retrocopy	retro_pabe_3195,
Pan troglodytes	ENSPTRG00000011705	1 retrocopy	retro_ptro_1347,
Pan troglodytes	ENSPTRG00000013164	1 retrocopy	retro_ptro_2745,
Pan troglodytes	ENSPTRG00000033886	1 retrocopy	retro_ptro_2668 ,