RetrogeneDB ID: retro_ptro_110

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:110447918..110448374(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039007
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SNX22
• Ensembl ID: ENSPTRG00000007155
• Aliases: None
• Description: sorting nexin 22 [Source:HGNC Symbol;Acc:16315]

Sequence

>retro_ptro_110
GGGAAGGAGGTGTTTAAGATAGAAGTGCTAATGAATGGAAGAAAACATTTTGTTGAAAAGAGATACAGCGAATTTCATGC
TTTACACAAAAAGCTTAAGAAATGTATAAAAACTCCAGAAATCCCTTCTAAACATGTTAGGAACTGGGTCCCCAAAGTCT
TGGAACAGCGACGACAAGGCTTGGAAACATACTTACAGGCTGTCATTTTAGAAAATGAAGAACTTCCCAAACTGTTTCTT
GATTTCCTAAATGTGCGACACTTGCCCTCTCTACCAAAGGCAGAAAGTTGTGGATCTTTTGATGAAACAGAGTCTGAAGA
GTCAAGCAAACTGTCCCACCAGCCTGTGCTGCTGTTCCTCAGGGATCCATATGTCTTGCCTGCAGCCAGCGATTTTCCAA
ATGTGGTTATTGAAGGAGTCCTCCATGGGATATTTTACCCTCATCTACAGCCCAGG

Alignment

ORF - retro_ptro_110 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.67 %
• Parental protein coverage: 77.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFRVEVLCSGRRHTVPRRYSEFHALHKRIKKLYKVPDFPSKRLPNWRTRGLEQRRQGLEAYIQGILYLNQ
          VF..EVL..GR.H.V..RYSEFHALHK..KK..K.P..PSK...NW....LEQRRQGLE.Y.Q.....N.
Retrocopy VFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENE

Parental  EVPKELLEFLRLRHFPTDPKASNWGTVREFLPGDSSSQQHQRPVLSFHVDPYVCNPSPESLPNVVVNGVL
          E.PK..L.FL..RH.P..PKA...G...E.....SS...HQ.PVL.F..DPYV..P.....PNVV..GVL
Retrocopy ELPKLFLDFLNVRHLPSLPKAESCGSFDETESEESSKLSHQ-PVLLFLRDPYVL-PAASDFPNVVIEGVL

Parental  QGLYSFSISP
          .G.......P
Retrocopy HGIFYPHLQP

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	2.04 RPM	11.71 RPM
SRP007412_cerebellum	1.36 RPM	3.98 RPM
SRP007412_heart	0.79 RPM	0.32 RPM
SRP007412_kidney	3.71 RPM	0.34 RPM
SRP007412_liver	1.70 RPM	0.92 RPM
SRP007412_testis	1.37 RPM	0.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_110 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_110 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_110 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000004181	1 retrocopy	retro_fcat_22,
Pan troglodytes	ENSPTRG00000007155	1 retrocopy	retro_ptro_110 ,