RetrogeneDB ID: retro_ptro_1905

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:89711164..89711586(-)
• Located in intron of: ENSPTRG00000042169

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX5
• Ensembl ID: ENSPTRG00000005034
• Aliases: None
• Description: None

Sequence

>retro_ptro_1905
ATGGGAAAGAAAACCAAGCACACAGCTAACAGTTCATCAGAGAATGAAGAGGAGTACACTGTGGAGAAGGTGCTAGACAG
GCATGTGGTTAAGGGGCAAGTGGAGTATCTGCTGAAGTGGAAAGGCTTTTCTGAGGAGCACAATATTTGGGAATCTGAGA
AAAACTTGGATTGCCTTTAGCTCATTTCTTAGTTTACAAAAAAGTTTAAGATGATGAAGGAGGGTTAAAACAACAAGCCT
GGGGAGAAGTCAGAAAGTAGCAAAGAAATCCAATTTCTCAAACTGTGCTGACAGTATCAAGTCCAAAAAAGAGAACAGAG
TGATGATATTGCTTGGGGCTTCGAGATAAGACTAGAACCAGAAAAGATCATTGGGGCAACAGATTCCTGTGGCAATTTAT
GTTTTTAATGAAATGGAAAGAC

Alignment

ORF - retro_ptro_1905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.34 %
• Parental protein coverage: 75.39 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKKTKRTADSSSSEDEEEYVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISEFMKKY
          MGKKTK.TA.SSS.E.EEEY.VEKVLDR.VVKGQVEYLLKWKGFSEEHN.WE.EKNLDC..LIS.F.KK.
Retrocopy MGKKTKHTANSSS-ENEEEYTVEKVLDRHVVKGQVEYLLKWKGFSEEHNIWESEKNLDCL*LIS*FTKKF

Parental  KKMKEGENNKPREKSESNKRKSNFSNSADDIKSKKKREQSNDIARGFERGLEPEKIIGATDSCGDL-MFL
          K.MKEG.NNKP.EKSES.K....F..........K.......IA.GFE..LEPEKIIGATDSCG.L.MFL
Retrocopy KMMKEG*NNKPGEKSESSK-EIQFLKLC*QYQVQKREQSDD-IAWGFEIRLEPEKIIGATDSCGNL<MFL

Parental  MKWKD
          MKWKD
Retrocopy MKWKD

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	11.24 RPM
SRP007412_cerebellum	0.07 RPM	28.89 RPM
SRP007412_heart	0.03 RPM	18.33 RPM
SRP007412_kidney	0.03 RPM	13.18 RPM
SRP007412_liver	0.00 RPM	6.09 RPM
SRP007412_testis	0.00 RPM	121.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1905 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1905 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1905 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2811
Gorilla gorilla	retro_ggor_1955
Pongo abelii	retro_pabe_2307

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018847	1 retrocopy	retro_cjac_2020,
Echinops telfairi	ENSETEG00000001220	1 retrocopy	retro_etel_678,
Homo sapiens	ENSG00000094916	1 retrocopy	retro_hsap_2811,
Gorilla gorilla	ENSGGOG00000000041	1 retrocopy	retro_ggor_1955,
Nomascus leucogenys	ENSNLEG00000017671	1 retrocopy	retro_nleu_428,
Pongo abelii	ENSPPYG00000004599	1 retrocopy	retro_pabe_2307,
Pan troglodytes	ENSPTRG00000005034	1 retrocopy	retro_ptro_1905 ,
Pan troglodytes	ENSPTRG00000019003	10 retrocopies	retro_ptro_17, retro_ptro_1706, retro_ptro_1875, retro_ptro_2289, retro_ptro_2475, retro_ptro_395, retro_ptro_537, retro_ptro_630, retro_ptro_729, retro_ptro_780,
Tursiops truncatus	ENSTTRG00000004524	1 retrocopy	retro_ttru_1859,