RetrogeneDB ID: retro_ptro_2475

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:117580053..117580597(-)
• Located in intron of: None

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_2475
ATGGCCTCCAATAAAACTACATTGTGAAAAATGGGGAAAAAAACAGAATGGGAAAAGTAAAAAGTTGAAGAGGCAGAGCC
TGAAGAATTTGCGGTGGAAAAAGTACTAGATTGACGTGTAGTGAATGGGAAAGTGGAATATTCCCTGAAGTGGAAGGGAT
TTACAGATGCTGACAATACTTGGGAACCTGAAGAAAATTTAGATTGTCCAGAATTGATTGAAGCATTTCTTAGCTCTCAG
AAAGCTGGCAAACAAAAAGATGGTAAAAAAGAAAATATCTGACAGTGAATCTGATGACAGCAAATCAAAGAAGAAAACAG
ATGCTGCTGACAAACCAAGAGGATTTGCCAGAGGTCTTGATCCTGAAAGAATAATTGGTGCCACAGACAGCAGTGGAGAA
TTGATGTTTCTCATGAAATGGAAAGATTCAGATGAGGCAGACTTGGTGCTGGCAAAAGAAGCAAGTATGAAGTGTCCTCA
AATTGTAATTGCTTTTTATGAAGAGAGACTAACTTGGCATTCTTGTCCAGAAGATGAAGCTCAA

Alignment

ORF - retro_ptro_2475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.52 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASNKTTLQKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCP
          MASNKTTL..............EEAEPEEF.VEKVLD.RVVNGKVEY.LKWKGFTDADNTWEPEENLDCP
Retrocopy MASNKTTLXXXXXXXXXXXXXXEEAEPEEFAVEKVLD*RVVNGKVEYSLKWKGFTDADNTWEPEENLDCP

Parental  ELIEA-FLNSQKAGKEKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFL
          ELIEA.FL...K....K.....K..SDSESDDSKSKKK.DAADKPRGFARGLDPERIIGATDSSGELMFL
Retrocopy ELIEA>FLALRKLANKK--MVKKKISDSESDDSKSKKKTDAADKPRGFARGLDPERIIGATDSSGELMFL

Parental  MKWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ
          MKWKDSDEADLVLAKEA.MKCPQIVIAFYEERLTWHSCPEDEAQ
Retrocopy MKWKDSDEADLVLAKEASMKCPQIVIAFYEERLTWHSCPEDEAQ

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	0.05 RPM	31.98 RPM
SRP007412_liver	0.03 RPM	21.93 RPM
SRP007412_testis	0.21 RPM	73.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2475 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2475 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2475 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3650
Gorilla gorilla	retro_ggor_2466
Pongo abelii	retro_pabe_2997

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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,