RetrogeneDB ID: retro_ptro_952

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:19446839..19447550(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTCD2
• Ensembl ID: ENSPTRG00000016968
• Aliases: None
• Description: Pan troglodytes pentatricopeptide repeat domain 2 (PTCD2), mRNA. [Source:RefSeq mRNA;Acc:NM_001246655]

Sequence

>retro_ptro_952
CTCATGAAAGACCAGCATTTATGAGATTCCTTCTCAGATTCCACATCGTTCAATATTTTGATGGATATGTTATTTATCCA
AGGCAAATATCAAAGTGCTTTGGAAGTATTGATAGAGATGAAAAATCAAGGTGTGAAATTCACCAAAGATCCTATGTTCT
TAGTTTTGCAGTTTGCAACAAACTGAAGAGCCCTGAGTCTTTCAAAATCTGTTCTACATTAAGAGAAGAAGCCCCACTCA
AAGGAGAGGTTCTCTCCAGGAGAGCATCCCGTTTCTTTGTGGTGTTAGCTCTGAATCAGAACCAAGTGGCAAAAGCTATG
TCCATTTTTTTCTCAAACCATGAATCCAGAAAGCATAGCCTGCACTAACTTAACTATTATAATCCATATCCAGTCAAATA
TGTTGGAAACCCTGATAGAGACACTAAAAAAATGCTGCAGAAGGAAATTTATTAAAATTTGTGAAAAGACATGCGTTCTC
AGAGGAAGTGCTGGCAAAAGTGAAGGAAAAGTGAAGGATATGCCTGCCCTTGTGGCCAGATTTAATGAGATCTATGGAAA
ACTGCACATCAGTGGCCAGGTAACCACTTGTACTTTGGGTACTCTGCTCTGCCACACCCCCAGGGACAGGAGATCCCATA
TGTTGCTATTAAACAAGAGGATGATGAGCCATTGGACCTTCCAGCCACTCAACCAGTCCTTTTTGGCTGAG

Alignment

ORF - retro_ptro_952 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.25 %
• Parental protein coverage: 61.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LMKDQHLRGFFSDSTSFNILMDMLFIKGKYKSALQVLIEMKNQDVKFTKD-TYVLAFAICYKLNSPESFK
          LMKDQHL...FSDSTSFNILMDMLFI.GKY.SAL.VLIEMKNQ.VKFTKD..YVL.FA.C.KL.SPESFK
Retrocopy LMKDQHL*DSFSDSTSFNILMDMLFIQGKYQSALEVLIEMKNQGVKFTKD<SYVLSFAVCNKLKSPESFK

Parental  ICTTLREEALLKGEILSRRASCFAVALALNQNEMAKAMSIF-SQIMNPESIACINLNIIIHIQSNMLENL
          IC.TLREEA.LKGE.LSRRAS.F.V.LALNQN..AKAMSIF.SQ.MNPESIAC.NL.IIIHIQSNMLE.L
Retrocopy ICSTLREEAPLKGEVLSRRASRFFVVLALNQNQVAKAMSIF>SQTMNPESIACTNLTIIIHIQSNMLETL

Parental  IKTL-KNAAEGNLSKFVRRHVFSEEVLAKVRE-KVKDVPALVAKFDEIYGTLHITGQVTTDSLDAVLCHT
          I.TL.KNAAEGNL.KFV.RH.FSEEVLAKV.E.KVKD.PALVA.F.EIYG.LHI.GQVTT..L...LCHT
Retrocopy IETL>KNAAEGNLLKFVKRHAFSEEVLAKVKE<KVKDMPALVARFNEIYGKLHISGQVTTCTLGTLLCHT

Parental  PRDRKSHTLLLNKRMVSRRTFQPLSQSLLAE
          PRDR.SH.LLLNKRM.S..TFQPL.QS.LAE
Retrocopy PRDRRSHMLLLNKRMMSHWTFQPLNQSFLAE

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	8.47 RPM
SRP007412_cerebellum	0.00 RPM	8.60 RPM
SRP007412_heart	0.00 RPM	8.51 RPM
SRP007412_kidney	0.00 RPM	9.96 RPM
SRP007412_liver	0.00 RPM	4.39 RPM
SRP007412_testis	0.11 RPM	6.01 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_952 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_952 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_952 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1388

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016364	1 retrocopy	retro_cjac_1598,
Homo sapiens	ENSG00000049883	2 retrocopies	retro_hsap_1388, retro_hsap_607,
Gorilla gorilla	ENSGGOG00000010695	2 retrocopies	retro_ggor_1077, retro_ggor_534,
Macaca mulatta	ENSMMUG00000017908	1 retrocopy	retro_mmul_2240,
Nomascus leucogenys	ENSNLEG00000004516	2 retrocopies	retro_nleu_2954, retro_nleu_436,
Otolemur garnettii	ENSOGAG00000008390	1 retrocopy	retro_ogar_3169,
Pan troglodytes	ENSPTRG00000016968	2 retrocopies	retro_ptro_447, retro_ptro_952 ,
Ictidomys tridecemlineatus	ENSSTOG00000006596	1 retrocopy	retro_itri_1469,