RetrogeneDB ID: retro_ptro_447

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:88388918..88389640(+)
• 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_447
ATAGTCTGAGACAGTATGGCTGCGGCATTTTGGTCCTCCAGATGAGCTCTTCTGCCAGCACTGCAGATTTCAGTGTATCC
CGGGATGAGAGGCTCCGGCTCCACCTGCTGCCACTGTCCTCTTGGAGCAAAAAGATATCTACTTACAGATAATATTATGA
AATTAAAAGAATTTCAGCATAAGAAGGTGGCTGTTGAATATAATCTTCCTGGCACCAAAGAAATCTATTTTAGAAACTTG
GAAGAGAAATTGAACTAGAACAAGCTCATCTTGAAGGGGAAGTTGAGAACCCTACTTCATTTGCGTGAGTCCTGGGACCA
TGTGGAACTGGCTAAAAACATCAATTGCAAGTACCATACAGAAAACAAAAATGTCACTTTGGCGGAATTTAAGTTTGGAC
CACTTTTCATAAGACTGTGTTACGACTTGAATCTTGAGGAATCTGCAATGGAGCTCAGGAAAGATGAGTATTTACAACGG
TTCTCAGACTCCACACAATTTACTGTTTTGATGGTTATGTTATTTATCAAAAGCAAATATATAAGTGCTTTGGAAATATT
GACAGAGATGAAAAACCCAGATGGAAAGTTCACCAGAATACCTATGTTCTTGATTTTGCAATTGGCTACAGACTGAATAG
CTCTGAATCTTTCAAAGTCTGTACTACATTAAGAAAAGAAGCCCTAATCAAAGGAGTTCTCTCCAGGAGAGCATCCTGTT
TC

Alignment

ORF - retro_ptro_447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.31 %
• Parental protein coverage: 62.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVRDSMAAAFRPSNRVLLQALQILVYPGVGGSGSVSCRCPLGAKRYLLTDNVVKLKEFQQKKVAVACNLS
          .V.DSMAAAF..S...LL.ALQI.VYPG..GSGS..C.CPLGAKRYLLTDN..KLKEFQ.KKVAV..NL.
Retrocopy IV*DSMAAAFWSSR*ALLPALQISVYPGMRGSGSTCCHCPLGAKRYLLTDNIMKLKEFQHKKVAVEYNLP

Parental  GTKETYFRNLKKKLTQNKLILKGELITLLHLCESRDHVELAKNVIYRYHAENKNFTLGEYKFGPLFVRLC
          GTKE.YFRNL..KL..NKLILKG.L.TLLHL.ES.DHVELAKN....YH.ENKN.TL.E.KFGPLF.RLC
Retrocopy GTKEIYFRNLEEKLN*NKLILKGKLRTLLHLRESWDHVELAKNINCKYHTENKNVTLAEFKFGPLFIRLC

Parental  YELDLEESAVELMKDQHLRGFFSDSTSFNILMDMLFIKGKYKSALQVLIEMKNQDVKFTK-DTYVLAFAI
          Y.L.LEESA.EL.KD..L...FSDST.F..LM.MLFIK.KY.SAL..L.EMKN.D.KFT...TYVL.FAI
Retrocopy YDLNLEESAMELRKDEYLQR-FSDSTQFTVLMVMLFIKSKYISALEILTEMKNPDGKFTR<NTYVLDFAI

Parental  CYKLNSPESFKICTTLREEALLKGEILSRRASCF
          .Y.LNS.ESFK.CTTLR.EAL.KG..LSRRASCF
Retrocopy GYRLNSSESFKVCTTLRKEALIKG-VLSRRASCF

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	0.11 RPM	8.60 RPM
SRP007412_heart	0.00 RPM	8.51 RPM
SRP007412_kidney	0.03 RPM	9.96 RPM
SRP007412_liver	0.00 RPM	4.39 RPM
SRP007412_testis	0.32 RPM	6.01 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_447 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_447 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_447 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_607
Gorilla gorilla	retro_ggor_534

---

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,