RetrogeneDB ID: retro_ptro_775

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:85893831..85894389(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TM2D3
• Ensembl ID: ENSPTRG00000007515
• Aliases: None
• Description: None

Sequence

>retro_ptro_775
GCAGTGAAAGTACCGAAATTACACCTTTTATGTTCAAGCAATGGTTTGTGTAGCAGGTATTCTGCAGAATTTATAGACTG
CACAACAAATGTCCTCTGTGTCTATGGGAAGCTAGTCACTTTTGACTGTACAGTGAAACCTTCTGTTGCCTGTGTTGATT
AGGAGTTAAAATCCCAAAGTAACTTTCTCATCAACATGACTTGATTTTGATGGAAGCCTCCAGAAACAGAATATGAATGT
TTCAATTCTACCAGCTGCATGAGGTCCTGTCCTCAACGGCATTATGCTGCCAAATACATGATAAACACATTCATGACTTG
GGTAACTACTTTTTTCAAAATGCTGCACTGAAATTGGGCTGGAGGCTATAAGTGGTCTATTGCTCTGGCTCTAAGCATCA
CCCTTGGTGGCTTTGGAGCAGACCATTTCCACCTCAACCAGTGGCAAGAAGGCCTTGGCAAGCTCTTCAGCTTCAGTGGC
CTGGAAATATGGACACTAATAGACATCTTGCTAATTGGAGTTGGCTACATTGGACCAGCAGATGGCTCTTGATACATT

Alignment

ORF - retro_ptro_775 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.26 %
• Parental protein coverage: 76.92 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STEIPPYVMKCPSNGLCSRLPADCIDCTTNFSCIYGKPVTFDCAVKPSVTCVDQDFKSQKNFIINMTCRF
          ....P.....C.SNGLCSR..A..IDCTTN..C.YGK.VTFDC.VKPSV.CVD...KSQ.NF.INMT..F
Retrocopy AVKVPKLHLLCSSNGLCSRYSAEFIDCTTNVLCVYGKLVTFDCTVKPSVACVD*ELKSQSNFLINMT*-F

Parental  CWQLPETDYECTNSTSCMTVSCPRQRYPANCTVRDHVHCLGNRTFPKMLYCNWTGGYKWSTALALSITLG
          .W..PET.YEC.NSTSCM..SCP...Y.A..............TF.KML..NW.GGYKWS.ALALSITLG
Retrocopy *WKPPETEYECFNSTSCMR-SCPQRHYAAKYMINTFMTWV--TTFFKMLH*NWAGGYKWSIALALSITLG

Parental  GFGADRFYLGQWREGLGKLFSFGGLGIWTLIDVLLIGVGYVGPADGSLYI
          GFGAD.F.L.QW.EGLGKLFSF.GL.IWTLID.LLIGVGY.GPADGS.YI
Retrocopy GFGADHFHLNQWQEGLGKLFSFSGLEIWTLIDILLIGVGYIGPADGS*YI

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	28.24 RPM
SRP007412_cerebellum	0.00 RPM	23.12 RPM
SRP007412_heart	0.00 RPM	13.84 RPM
SRP007412_kidney	0.00 RPM	15.66 RPM
SRP007412_liver	0.00 RPM	18.10 RPM
SRP007412_testis	0.00 RPM	8.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_775 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_775 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_775 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1138
Gorilla gorilla	retro_ggor_887
Macaca mulatta	retro_mmul_884

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017340	1 retrocopy	retro_cjac_3233,
Homo sapiens	ENSG00000184277	1 retrocopy	retro_hsap_1138,
Gorilla gorilla	ENSGGOG00000011598	1 retrocopy	retro_ggor_887,
Macaca mulatta	ENSMMUG00000000277	1 retrocopy	retro_mmul_884,
Mustela putorius furo	ENSMPUG00000010985	1 retrocopy	retro_mputfur_313,
Nomascus leucogenys	ENSNLEG00000000529	1 retrocopy	retro_nleu_937,
Pan troglodytes	ENSPTRG00000007515	1 retrocopy	retro_ptro_775 ,
Tarsius syrichta	ENSTSYG00000004536	1 retrocopy	retro_tsyr_1116,