RetrogeneDB ID: retro_ptro_583

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:348121..348380(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS24
• Ensembl ID: ENSPTRG00000019127
• Aliases: None
• Description: None

Sequence

>retro_ptro_583
ATGGCGGCCTCCGTGTGCGGCGGGTGGCGGGGGCCCCGGGTGCTGTCCTGGGGCCGAGAGCCGCCTTGCGCGGGGCGGGC
CCTGCACACCTCCGCGGTCTGTAACAAGAACCGGCGGCCCGAGTCCGCGGAGGCCAGGAGGACAAGCCGGTGACCTATGA
GGACGCACACGCGCCGCACTTCGTCGCCCGCCATGAGGGCCAGAGGTCGCTCACGCGGGGAACCCTGGTGGGGAGGACCA
CGCGGCGGAGCGAACGGTG

Alignment

ORF - retro_ptro_583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.79 %
• Parental protein coverage: 52.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASVCSGLLGPRVLSWSRELPCAWRALHTSPVCAKNR-AARVRVSKGDKAVTYEEAHAPHYIAHRKGWL
          MAASVC.G..GPRVLSW.RE.PCA.RALHTS.VC.KNR.AARVR....DK.VTYE.AHAPH..A...G..
Retrocopy MAASVCGGWRGPRVLSWGREPPCAGRALHTSAVCNKNR<AARVRGGQEDKPVTYEDAHAPHFVARHEGQR

Parental  SL-HTGNLDGEDHAAERTV
          SL.H.GN..GEDHAAERTV
Retrocopy SL<HAGNPGGEDHAAERTV

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	28.85 RPM
SRP007412_cerebellum	0.00 RPM	17.82 RPM
SRP007412_heart	0.00 RPM	23.90 RPM
SRP007412_kidney	0.00 RPM	33.00 RPM
SRP007412_liver	0.03 RPM	31.78 RPM
SRP007412_testis	0.00 RPM	18.23 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_583 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_583 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_583 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017491	1 retrocopy	retro_amel_1126,
Bos taurus	ENSBTAG00000007398	1 retrocopy	retro_btau_411,
Choloepus hoffmanni	ENSCHOG00000003106	1 retrocopy	retro_chof_2334,
Dasypus novemcinctus	ENSDNOG00000016853	3 retrocopies	retro_dnov_1195, retro_dnov_153, retro_dnov_2049,
Echinops telfairi	ENSETEG00000016782	1 retrocopy	retro_etel_1350,
Homo sapiens	ENSG00000062582	1 retrocopy	retro_hsap_836,
Gorilla gorilla	ENSGGOG00000005692	1 retrocopy	retro_ggor_687,
Loxodonta africana	ENSLAFG00000011905	1 retrocopy	retro_lafr_426,
Macaca mulatta	ENSMMUG00000002405	1 retrocopy	retro_mmul_1089,
Monodelphis domestica	ENSMODG00000013889	1 retrocopy	retro_mdom_1785,
Pan troglodytes	ENSPTRG00000019127	1 retrocopy	retro_ptro_583 ,
Pteropus vampyrus	ENSPVAG00000015911	4 retrocopies	retro_pvam_1129, retro_pvam_1360, retro_pvam_180, retro_pvam_978,
Tursiops truncatus	ENSTTRG00000002938	1 retrocopy	retro_ttru_1860,