RetrogeneDB ID: retro_ptro_2862

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:122818727..122818917(+)
• Located in intron of: ENSPTRG00000021349

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM5
• Ensembl ID: ENSPTRG00000019057
• Aliases: None
• Description: None

Sequence

>retro_ptro_2862
ATGGCGGCTAAGGCTACCACCTACTTGCCCAGCTGTTGCTGCTAGAGCTTGTAGACAAATGTATAGGCTCAAGAATTCAC
ATTGTGGTGAAGAGTCATTAAGAAATCGTGGGTACTCTTCTAGGAGTTGATGACTTTGTCAATATGGACTAGAAGAGGTC
ACTGAGTTTGAAATCACACCAGAAGGAAGA

Alignment

ORF - retro_ptro_2862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.3 %
• Parental protein coverage: 70.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAANATTNP-SQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNM-VLEDVTEFEITPEGR
          MAA.ATT....QLL.LELVDKCIGSRIHIV.KS..EIVGTLLG.DDFVNM..LE.VTEFEITPEGR
Retrocopy MAAKATTYL<AQLLLLELVDKCIGSRIHIVVKSH*EIVGTLLGVDDFVNM<GLEEVTEFEITPEGR

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	8.28 RPM
SRP007412_cerebellum	0.00 RPM	4.09 RPM
SRP007412_heart	0.00 RPM	7.49 RPM
SRP007412_kidney	0.00 RPM	9.60 RPM
SRP007412_liver	0.03 RPM	4.58 RPM
SRP007412_testis	0.00 RPM	5.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2862 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2862 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4216
Gorilla gorilla	retro_ggor_2824
Pongo abelii	retro_pabe_3449

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006700	1 retrocopy	retro_amel_453,
Callithrix jacchus	ENSCJAG00000009185	3 retrocopies	retro_cjac_1883, retro_cjac_2760, retro_cjac_3068,
Cavia porcellus	ENSCPOG00000010421	1 retrocopy	retro_cpor_607,
Equus caballus	ENSECAG00000018445	1 retrocopy	retro_ecab_809,
Echinops telfairi	ENSETEG00000018068	8 retrocopies	retro_etel_1305, retro_etel_1502, retro_etel_1907, retro_etel_198, retro_etel_2054, retro_etel_2193, retro_etel_454, retro_etel_964,
Mus musculus	ENSMUSG00000091625	4 retrocopies	retro_mmus_1568, retro_mmus_423, retro_mmus_826, retro_mmus_837,
Nomascus leucogenys	ENSNLEG00000015268	1 retrocopy	retro_nleu_179,
Otolemur garnettii	ENSOGAG00000013892	3 retrocopies	retro_ogar_2727, retro_ogar_3062, retro_ogar_881,
Pongo abelii	ENSPPYG00000017661	1 retrocopy	retro_pabe_3449,
Pan troglodytes	ENSPTRG00000019057	1 retrocopy	retro_ptro_2862 ,
Pteropus vampyrus	ENSPVAG00000009786	1 retrocopy	retro_pvam_1410,
Rattus norvegicus	ENSRNOG00000042126	3 retrocopies	retro_rnor_1171, retro_rnor_567, retro_rnor_694,
Tupaia belangeri	ENSTBEG00000004876	11 retrocopies	retro_tbel_1043, retro_tbel_1107, retro_tbel_1217, retro_tbel_1323, retro_tbel_1549, retro_tbel_1865, retro_tbel_2203, retro_tbel_2908, retro_tbel_2956, retro_tbel_3330, retro_tbel_4335,
Tursiops truncatus	ENSTTRG00000004237	3 retrocopies	retro_ttru_1521, retro_ttru_1585, retro_ttru_874,