RetrogeneDB ID: retro_ptro_3268

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:132397096..132397539(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM195A
• Ensembl ID: ENSPTRG00000007548
• Aliases: None
• Description: Pan troglodytes family with sequence similarity 195, member A (FAM195A), mRNA. [Source:RefSeq mRNA;Acc:NM_001251932]

Sequence

>retro_ptro_3268
CTGTACACCATCATCAACGGGCCCAGCAAGTTGGTCGCGCAGCGCCGCACAGGTCTCACGCAGCAGCAGGTGAAGGGCCA
GCTCCAGGAGCTCCTGAAAAGCCGGCAGCCCGCGCCGCCGACCTTGCAGCCCCAGCGGGCGCAGCCCTTCGCGCAGCCGC
TGGGACCCTGGCCCCTGTCGAGTCCAGGGCCAAGGCTTGTGTTCAATCGTGTGAATCGCCGGCGGGACCCCTCCAAGTCC
GCATCCCTCCAGGGGACCCAGGAGACCTACACACTGGCCCACAAGGAGAATGTCCGCTTTGTGTCCGAAGCCTGGCAGCA
GGTGCGGCAGCAGCTGGATGGTGGCCCAGCCGGTGAGGGCGGGACAAGGCCTGTGCAGTGGAGAGGATCCCCAATCCCCG
GCTGCAGAACTTCGTGCCCATTGACTTGGACGAGTGGTGGGCG

Alignment

ORF - retro_ptro_3268 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.67 %
• Parental protein coverage: 76.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MYTITKGPSKLVAQRRTGPTQQQVEGRLGELLKCRQPAPPTSQPPRAQPFAQPPGPWPLSSPGPRLVFNR
          .YTI..GPSKLVAQRRTG.TQQQV.G.L.ELLK.RQPAPPT.QP.RAQPFAQP.GPWPLSSPGPRLVFNR
Retrocopy LYTIINGPSKLVAQRRTGLTQQQVKGQLQELLKSRQPAPPTLQPQRAQPFAQPLGPWPLSSPGPRLVFNR

Parental  VNGRRAPSTSPSFEGTQETYTVAHEENVRFVSEAWQQVQQQLDSGPAGEGGPRPVQYVERTPNP-RLQNF
          VN.RR.PS.S.S..GTQETYT.AH.ENVRFVSEAWQQV.QQLD.GPAGEGG.RPVQ.....P.P.RLQNF
Retrocopy VNRRRDPSKSASLQGTQETYTLAHKENVRFVSEAWQQVRQQLDGGPAGEGGTRPVQW-RGSPIP<RLQNF

Parental  VPIDLDEWWA
          VPIDLDEWWA
Retrocopy VPIDLDEWWA

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	12.58 RPM
SRP007412_cerebellum	0.00 RPM	5.23 RPM
SRP007412_heart	0.00 RPM	3.70 RPM
SRP007412_kidney	0.00 RPM	43.62 RPM
SRP007412_liver	0.00 RPM	11.23 RPM
SRP007412_testis	0.00 RPM	2.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3268 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3268 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3268 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4901

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011979	1 retrocopy	retro_cjac_932,
Homo sapiens	ENSG00000172366	1 retrocopy	retro_hsap_4901,
Gorilla gorilla	ENSGGOG00000013784	1 retrocopy	retro_ggor_43,
Nomascus leucogenys	ENSNLEG00000008117	1 retrocopy	retro_nleu_1269,
Pan troglodytes	ENSPTRG00000007548	1 retrocopy	retro_ptro_3268 ,
Sus scrofa	ENSSSCG00000007995	1 retrocopy	retro_sscr_433,