RetrogeneDB ID: retro_ptro_780

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:95525145..95525669(-)
• Located in intron of: ENSPTRG00000005312

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX3
• Ensembl ID: ENSPTRG00000019003
• Aliases: None
• Description: None

Sequence

>retro_ptro_780
ATGGCCTCCAACAAAACCACATTGCAAAACATGGGAAAGAAACAGAATGGAAAAGTAAAAAAGTTGAAAAGGCAGAGCCT
GAAGAATTTGTGGTGGAAAATGTACCAGATAGACATGCAGGGAATGGGAAAGTGGAATATTTCCTGAAGGAATTTACAGA
TGCTGACAATACTTTGGAACCTGAAGAAAATTTAGATTGTCCAGAGTTAATTGAAGCATTTCTTAATTCTCAAAAAGCTG
GTGAAGAAAAAGATGGTACAAAAAGAAAACCTTTATCTGGCAGTGAATCTGATGACAGCAAATCAAAGAAGAAAAGAGAT
GCTGTTGACAAACCAAGAGGAATTGCCAGAGGTCTTGATCCTGAAAGAATAATTGGTGCCACAGATGGCAGTGAAGAATT
GATGTTGCTCATGAAATGGAAGGATTCAGATGAGGCAGACTTGGTGCTGGCACAAAAGGCAAATATGAAGTATCCTCAAA
TTGAAATTGCTTTTTATGAAGAAAGACTAACTTGGCATTCTTGT

Alignment

ORF - retro_ptro_780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.52 %
• Parental protein coverage: 96.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASNKTTLQKMGKKQNGK-SKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDC
          MASNKTTLQ.MGKKQNGK.SKKVE.AEPEEFVVE.V.DR...NGKVEYFLK...FTDADNT.EPEENLDC
Retrocopy MASNKTTLQNMGKKQNGK<SKKVEKAEPEEFVVENVPDRHAGNGKVEYFLK--EFTDADNTLEPEENLDC

Parental  PELIEAFLNSQKAGKEKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFL
          PELIEAFLNSQKAG.EKDGTKRK.LS.SESDDSKSKKKRDA.DKPRG.ARGLDPERIIGATD.S.ELM.L
Retrocopy PELIEAFLNSQKAGEEKDGTKRKPLSGSESDDSKSKKKRDAVDKPRGIARGLDPERIIGATDGSEELMLL

Parental  MKWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWHSC
          MKWKDSDEADLVLA..ANMK.PQI.IAFYEERLTWHSC
Retrocopy MKWKDSDEADLVLAQKANMKYPQIEIAFYEERLTWHSC

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	0.02 RPM	30.19 RPM
SRP007412_cerebellum	0.00 RPM	17.71 RPM
SRP007412_heart	0.00 RPM	22.38 RPM
SRP007412_kidney	0.03 RPM	31.98 RPM
SRP007412_liver	0.00 RPM	21.93 RPM
SRP007412_testis	0.00 RPM	73.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_780 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_780 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_780 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1145
Pongo abelii	retro_pabe_951
Callithrix jacchus	retro_cjac_3322

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002897	11 retrocopies	retro_cfam_1157, retro_cfam_161, retro_cfam_1811, retro_cfam_1823, retro_cfam_1849, retro_cfam_2083, retro_cfam_502, retro_cfam_594, retro_cfam_739, retro_cfam_931, retro_cfam_948,
Callithrix jacchus	ENSCJAG00000007952	8 retrocopies	retro_cjac_1100, retro_cjac_1414, retro_cjac_1612, retro_cjac_2405, retro_cjac_2623, retro_cjac_2728, retro_cjac_3322, retro_cjac_869,
Loxodonta africana	ENSLAFG00000006907	3 retrocopies	retro_lafr_661, retro_lafr_687, retro_lafr_776,
Mus musculus	ENSMUSG00000029836	1 retrocopy	retro_mmus_77,
Otolemur garnettii	ENSOGAG00000016583	1 retrocopy	retro_ogar_136,
Ochotona princeps	ENSOPRG00000011713	9 retrocopies	retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
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 ,
Pteropus vampyrus	ENSPVAG00000006297	2 retrocopies	retro_pvam_294, retro_pvam_786,
Rattus norvegicus	ENSRNOG00000011814	2 retrocopies	retro_rnor_120, retro_rnor_301,
Sarcophilus harrisii	ENSSHAG00000017913	1 retrocopy	retro_shar_153,
Sus scrofa	ENSSSCG00000016711	4 retrocopies	retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,