RetrogeneDB ID: retro_ptro_2284

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:109308126..109308411(-)
• Located in intron of: ENSPTRG00000017117

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM2
• Ensembl ID: ENSPTRG00000017986
• Aliases: None
• Description: None

Sequence

>retro_ptro_2284
ATGCTCTTCTATTATTTTTTCAAGTCCCTTGTGGGCAAGCATGTGGTCGTGGAACTCAAGAATGACCTGAGCATCTGTGG
AACCCTCCATTCTGTGGATCGGTATCTCAACATCAAACTAACTAATATCAGTGTCATAGACCCTGAGAAATATCCTCACA
TGTTATCAGTGAAGAACTGCTTCATTCAGGGCTCAGTGGTCCGATACATGCAGTTGCCAGCAGACGAGGTCCACAAACAG
TTGCTACAGGGTGCAGCAAGGAAGGAACCCTTGCAGCAGAAACAG

Alignment

ORF - retro_ptro_2284 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNCFIRGSVVRYV
          MLFY.FFKSLVGK.VVVELKNDLSICGTLHSVD.YLNIKLT.ISV.DPEKYPHMLSVKNCFI.GSVVRY.
Retrocopy MLFYYFFKSLVGKHVVVELKNDLSICGTLHSVDRYLNIKLTNISVIDPEKYPHMLSVKNCFIQGSVVRYM

Parental  QLPADEVDTQLLQDAARKEALQQKQ
          QLPADEV..QLLQ.AARKE.LQQKQ
Retrocopy QLPADEVHKQLLQGAARKEPLQQKQ

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	0.04 RPM	11.44 RPM
SRP007412_cerebellum	0.00 RPM	13.41 RPM
SRP007412_heart	0.00 RPM	7.72 RPM
SRP007412_kidney	0.00 RPM	15.53 RPM
SRP007412_liver	0.03 RPM	8.74 RPM
SRP007412_testis	0.00 RPM	9.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2284 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2284 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2284 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3361
Pongo abelii	retro_pabe_2765
Macaca mulatta	retro_mmul_2099
Callithrix jacchus	retro_cjac_1828

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002601	2 retrocopies	retro_cjac_1828, retro_cjac_2088,
Felis catus	ENSFCAG00000004511	1 retrocopy	retro_fcat_309,
Macaca mulatta	ENSMMUG00000006832	3 retrocopies	retro_mmul_1389, retro_mmul_1875, retro_mmul_2099,
Mus musculus	ENSMUSG00000007050	1 retrocopy	retro_mmus_931,
Nomascus leucogenys	ENSNLEG00000006371	1 retrocopy	retro_nleu_960,
Ochotona princeps	ENSOPRG00000003668	2 retrocopies	retro_opri_250, retro_opri_917,
Pongo abelii	ENSPPYG00000016461	1 retrocopy	retro_pabe_2765,
Pan troglodytes	ENSPTRG00000017986	3 retrocopies	retro_ptro_1349, retro_ptro_2063, retro_ptro_2284 ,
Rattus norvegicus	ENSRNOG00000048725	1 retrocopy	retro_rnor_1463,
Ictidomys tridecemlineatus	ENSSTOG00000013144	1 retrocopy	retro_itri_189,