RetrogeneDB ID: retro_ptro_2871

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:6749731..6750274(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF2
• Ensembl ID: ENSPTRG00000001775
• Aliases: None
• Description: None

Sequence

>retro_ptro_2871
CTGCAGCGAGGCAAGAAACAATAGATTGAAAATGGTAGTGGAGCAGAAGATAACGGTGACAGTTCACACTGTAGTAATGC
CTCCACACATAGCAATCAGGAAGCAGGCCCTAGTAACAAATGAACCAAAACAACTGATGATTCTGGGCTTGAGCTTGATA
ACAACAATGCAGCAATGGAAATTGATCCAGTAATGGATGGCGCTAGTGAAATCGAATTAATATTCAGGCCTCCTCCCACA
CTTATGGAAAAAGATGACAGTGCACAGACAAGATACATAAAGACTTCTGGTAACACCACTGTTGATTACTTATCCAAGTA
GCTGGCTGTGAGGTTAGCTTTAGAAGAACTTTGAAGCAAAGGTGAATCAAACCAGATGAGCCTTGATACAGCCAGTGAGA
AGCAGTATACCACTTATATAGTAACAGCCAGTGGCCAGTTCACTGTATTAAATTGCTCTTTTTCTTTGGAATTGGTCAGT
GAGAAATACTAGAAAGTGAACAAACCCATGGAACTTTACTATGCACATACAAGGGAGCACAAA

Alignment

ORF - retro_ptro_2871 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.61 %
• Parental protein coverage: 53.87 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQRGKKQQIENGSGAEDNGDSSHCSNASTHSNQEAGPSNKRTKTSDDSGLELDNNNAAMAIDPVMDGASE
          LQRGKKQ.IENGSGAEDNGDSSHCSNASTHSNQEAGPSNK.TKT.DDSGLELDNNNAAM.IDPVMDGASE
Retrocopy LQRGKKQ*IENGSGAEDNGDSSHCSNASTHSNQEAGPSNK*TKTTDDSGLELDNNNAAMEIDPVMDGASE

Parental  IELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYI
          IEL.FRP.PTLMEKDDSAQTRYIKTSGN.TVD.LSK.LAVRLALEEL.SKGESNQM.LDTASEKQYT.YI
Retrocopy IELIFRPPPTLMEKDDSAQTRYIKTSGNTTVDYLSK*LAVRLALEEL*SKGESNQMSLDTASEKQYTTYI

Parental  ATASGQFTVLNGSFSLELVSEKYWKVNKPMELYYAPTKEHK
          .TASGQFTVLN.SFSLELVSEKY.KVNKPMELYYA.T.EHK
Retrocopy VTASGQFTVLNCSFSLELVSEKY*KVNKPMELYYAHTREHK

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	0.05 RPM	9.47 RPM
SRP007412_cerebellum	0.11 RPM	9.32 RPM
SRP007412_heart	0.00 RPM	4.66 RPM
SRP007412_kidney	0.26 RPM	9.60 RPM
SRP007412_liver	0.00 RPM	4.55 RPM
SRP007412_testis	0.00 RPM	18.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2871 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2871 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2871 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4226

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011199	3 retrocopies	retro_chof_1450, retro_chof_2217, retro_chof_2251,
Callithrix jacchus	ENSCJAG00000005442	1 retrocopy	retro_cjac_4198,
Erinaceus europaeus	ENSEEUG00000014091	1 retrocopy	retro_eeur_88,
Echinops telfairi	ENSETEG00000015824	1 retrocopy	retro_etel_2081,
Felis catus	ENSFCAG00000009609	1 retrocopy	retro_fcat_1725,
Homo sapiens	ENSG00000121481	2 retrocopies	retro_hsap_4056, retro_hsap_4226,
Gorilla gorilla	ENSGGOG00000014400	1 retrocopy	retro_ggor_2724,
Loxodonta africana	ENSLAFG00000021357	1 retrocopy	retro_lafr_407,
Myotis lucifugus	ENSMLUG00000001129	1 retrocopy	retro_mluc_2187,
Monodelphis domestica	ENSMODG00000007422	1 retrocopy	retro_mdom_857,
Nomascus leucogenys	ENSNLEG00000018029	2 retrocopies	retro_nleu_1042, retro_nleu_554,
Oryctolagus cuniculus	ENSOCUG00000004892	1 retrocopy	retro_ocun_838,
Pongo abelii	ENSPPYG00000000417	2 retrocopies	retro_pabe_3331, retro_pabe_3374,
Pan troglodytes	ENSPTRG00000001775	2 retrocopies	retro_ptro_2749, retro_ptro_2871 ,
Ictidomys tridecemlineatus	ENSSTOG00000006625	3 retrocopies	retro_itri_1646, retro_itri_1794, retro_itri_410,
Tupaia belangeri	ENSTBEG00000016387	4 retrocopies	retro_tbel_1757, retro_tbel_3368, retro_tbel_3892, retro_tbel_4061,
Tarsius syrichta	ENSTSYG00000006109	6 retrocopies	retro_tsyr_1344, retro_tsyr_1647, retro_tsyr_2063, retro_tsyr_2083, retro_tsyr_227, retro_tsyr_474,