RetrogeneDB ID: retro_ptro_3220

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:54134963..54135494(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIPIN
• Ensembl ID: ENSPTRG00000007192
• Aliases: None
• Description: TIMELESS interacting protein [Source:HGNC Symbol;Acc:30750]

Sequence

>retro_ptro_3220
TCAGGAAGTGGAGCACTTGTTCCTGTACCTCCAAAGAGAGCAGTTAAAAGAAATATATCCAAGCTGGATGCTCACAGATT
AATTTCAGAGAGAGGGCTTCCAGCCTTAAGGCATGTATTTGATAAGGCAAAATTCAAAGGTAAAAGTCATGAGGCTGAAG
ACTTAAAGATGCTAATCAGACACATGGAACACTGGGCACGTAGGCAATTCCCTAAACTGCAGTTTGAGGATTTTATTGAC
AGAGTTGAATACCTGAGAAATAAAAAGGAAATTCAGACCTGTTTAAAATGAATTTGACTTGATCTCCCTATTTTACATGA
ATATGTTGTTAGCAATAATGAGGAAGTTGGGGAAAATAATGGACATGGTGTAACTGCTACTGAATTAGATCCCTTTCTGA
CAAACTCATCTGAAAGTGAGATGTTTGCTTCTGAGTCAAGTAGAAGCCTAACAGATGAGCAACAACAAAGGATTGAGAGA
AATAAACAACCGGCTTTGGAAAGAAGGCAGGCAAAGCTGCTGAGTAATAGT

Alignment

ORF - retro_ptro_3220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.75 %
• Parental protein coverage: 58.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGNAAPVPVPPKRTVKRNIPKLDAQRLISERGLPALRHVFDKAKFKGKGHEAEDLKMLIRHMEHWAHRLF
          SG..A.VPVPPKR.VKRNI.KLDA.RLISERGLPALRHVFDKAKFKGK.HEAEDLKMLIRHMEHWA.R.F
Retrocopy SGSGALVPVPPKRAVKRNISKLDAHRLISERGLPALRHVFDKAKFKGKSHEAEDLKMLIRHMEHWARRQF

Parental  PKLQFEDFIDRVEYLGSKKEVQT-LKRIRLDPPILHEDFVSNNDEVAENNEHDVTSTELDPFLTNLSESE
          PKLQFEDFIDRVEYL..KKE.QT.LK.I.LD.PILHE..VSNN.EV.ENN.H.VT.TELDPFLTN.SESE
Retrocopy PKLQFEDFIDRVEYLRNKKEIQTCLK*I*LDLPILHEYVVSNNEEVGENNGHGVTATELDPFLTNSSESE

Parental  MFASELSRSLTEEQQQRIERNKQLALERRQAKLLSNS
          MFASE.SRSLT.EQQQRIERNKQ.ALERRQAKLLSNS
Retrocopy MFASESSRSLTDEQQQRIERNKQPALERRQAKLLSNS

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	1.29 RPM
SRP007412_cerebellum	0.00 RPM	2.08 RPM
SRP007412_heart	0.00 RPM	0.76 RPM
SRP007412_kidney	0.00 RPM	1.39 RPM
SRP007412_liver	0.00 RPM	1.44 RPM
SRP007412_testis	0.00 RPM	14.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3220 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3220 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3220 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4837

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004860	1 retrocopy	retro_chof_223,
Dasypus novemcinctus	ENSDNOG00000003177	3 retrocopies	retro_dnov_1334, retro_dnov_1481, retro_dnov_410,
Homo sapiens	ENSG00000075131	1 retrocopy	retro_hsap_4837,
Gorilla gorilla	ENSGGOG00000000061	3 retrocopies	retro_ggor_1268, retro_ggor_2907, retro_ggor_3016,
Loxodonta africana	ENSLAFG00000026016	1 retrocopy	retro_lafr_1104,
Microcebus murinus	ENSMICG00000004386	2 retrocopies	retro_mmur_155, retro_mmur_255,
Macaca mulatta	ENSMMUG00000003695	1 retrocopy	retro_mmul_1582,
Nomascus leucogenys	ENSNLEG00000012909	1 retrocopy	retro_nleu_1336,
Pan troglodytes	ENSPTRG00000007192	2 retrocopies	retro_ptro_1145, retro_ptro_3220 ,
Rattus norvegicus	ENSRNOG00000043068	1 retrocopy	retro_rnor_364,