RetrogeneDB ID: retro_ptro_200

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:130609012..130609307(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGN3
• Ensembl ID: ENSPTRG00000018366
• Aliases: None
• Description: None

Sequence

>retro_ptro_200
ATGCAGAAGAGAAAGTCTCCAGAGAATACAGAGGGCAAAGATGGCTCCAAAGTAACTAAACAGGAGCCCACAAGATGGTC
TCCCAGATTGTCAGCAAAACCTCCTCCACCAAAACCTGGACCCAAACCAAGAAAAACATCTGCTAAGAAAGAACCTGGAG
CAAAGGTTAGCAGAGGTGCTAAAGAGAAGAAAGGAAAAGTAGGAAGCTGGAAAGGAAGGTACTGCACCAGCTGAAAATGA
TGAAACTAAAGCTGAAGAGGCACAGAAAACTGAATCTGGAGATAACCAGGGAGAA

Alignment

ORF - retro_ptro_200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKRKSPENTEGKDGSKVTKQEPTRRSARLSAKPAPPKP-EPKPRKTSAKKEPGAKISRGAKGKKEEKQE
          M.KRKSPENTEGKDGSKVTKQEPTR.S.RLSAKP.PPKP..P...K....K..........K..KE.K.E
Retrocopy MQKRKSPENTEGKDGSKVTKQEPTRWSPRLSAKPPPPKP>DPNQEKHLLRKNLEQRLAEVLKRRKE-K*E

Parental  AGKEGTAPSENGETKAEEAQKTESVDNEGE
          AGKEGTAP.EN.ETKAEEAQKTES.DN.GE
Retrocopy AGKEGTAPAENDETKAEEAQKTESGDNQGE

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	25.33 RPM
SRP007412_cerebellum	0.04 RPM	29.43 RPM
SRP007412_heart	0.03 RPM	96.44 RPM
SRP007412_kidney	0.00 RPM	63.91 RPM
SRP007412_liver	0.03 RPM	29.46 RPM
SRP007412_testis	0.00 RPM	20.87 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_200 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_200 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_231
Pongo abelii	retro_pabe_421
Macaca mulatta	retro_mmul_414

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007015	1 retrocopy	retro_chof_2241,
Cavia porcellus	ENSCPOG00000012407	2 retrocopies	retro_cpor_1399, retro_cpor_147,
Felis catus	ENSFCAG00000028793	1 retrocopy	retro_fcat_1400,
Homo sapiens	ENSG00000118418	1 retrocopy	retro_hsap_231,
Gorilla gorilla	ENSGGOG00000006910	1 retrocopy	retro_ggor_293,
Macaca mulatta	ENSMMUG00000004351	1 retrocopy	retro_mmul_414,
Nomascus leucogenys	ENSNLEG00000012377	2 retrocopies	retro_nleu_68, retro_nleu_851,
Otolemur garnettii	ENSOGAG00000016487	1 retrocopy	retro_ogar_190,
Ochotona princeps	ENSOPRG00000009611	1 retrocopy	retro_opri_799,
Pan troglodytes	ENSPTRG00000018366	2 retrocopies	retro_ptro_1427, retro_ptro_200 ,
Ictidomys tridecemlineatus	ENSSTOG00000014353	1 retrocopy	retro_itri_251,
Tupaia belangeri	ENSTBEG00000015468	3 retrocopies	retro_tbel_1912, retro_tbel_4714, retro_tbel_615,
Tarsius syrichta	ENSTSYG00000005238	3 retrocopies	retro_tsyr_1569, retro_tsyr_268, retro_tsyr_976,