RetrogeneDB ID: retro_ggor_635

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 11:28208873..28209424(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000028388
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CBX3
• Ensembl ID: ENSGGOG00000025853
• Aliases: None
• Description: None

Sequence

>retro_ggor_635
ATAGCCTCCAATAAAACTACATGGCAAAAAATGAGAAAGAAACAGAATGGAAAGAATAAAAAGTTGAAGAGGCAGAGCCC
GAATAATTTGTGGTGGAAAAAGTACTAGATCGACGTGTAGTGAATGGGAAAGTGGAATATTTTCTGAAGTGGAAGGGATT
TACAGATGCTGACAATACTTGGGAATCTGAAGAAAATTTACATTGTCCAGAGTTGATTGAAGCATTTCTTAATTCTCAAA
AAGCTGGCAAAGAAAAAGTTGGTACAAAAAGAAAATCTTTATCTGACAGTGAATCTGATGACAGCAAATCAAAGAAGAAA
AGAGAAGCTGCTGACAAACCAAGAGGATTTGCCAGAGGTCGTGATCCTGAAAGAGTAATTGGTGCCACAGACGGCAGTGG
GGAATTGATGTTTCTCATGAAATGGAAAGATTCAGATGAGGCAGACTCAGTGCTGGCCTCAAAAGAGGCGAATATGAAGT
ATCCTCAAATTATAATTGCTTTTTATGAAGAGAGACTAACTTGGCATGCTTGTCCGGAAGATGAAGCTCAA

Alignment

ORF - retro_ggor_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.27 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASNKTTLQKMGKKQNGKSKK-VEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDC
          .ASNKTT.QKM.KKQNGK.KK.VEEAEPE.FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWE.EENL.C
Retrocopy IASNKTTWQKMRKKQNGKNKK<VEEAEPE*FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWESEENLHC

Parental  PELIEAFLNSQKAGKEKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFL
          PELIEAFLNSQKAGKEK.GTKRKSLSDSESDDSKSKKKR.AADKPRGFARG.DPER.IGATD.SGELMFL
Retrocopy PELIEAFLNSQKAGKEKVGTKRKSLSDSESDDSKSKKKREAADKPRGFARGRDPERVIGATDGSGELMFL

Parental  MKWKDSDEADLVLA-KEANMKCPQIVIAFYEERLTWHSCPEDEAQ
          MKWKDSDEAD.VLA.KEANMK.PQI.IAFYEERLTWH.CPEDEAQ
Retrocopy MKWKDSDEADSVLASKEANMKYPQIIIAFYEERLTWHACPEDEAQ

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	24.31 RPM
SRP007412_cerebellum	0.00 RPM	19.46 RPM
SRP007412_heart	0.00 RPM	5.22 RPM
SRP007412_kidney	0.00 RPM	38.68 RPM
SRP007412_liver	0.00 RPM	24.45 RPM
SRP007412_testis	0.10 RPM	88.58 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_635 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_635 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_766
Pan troglodytes	retro_ptro_537
Pongo abelii	retro_pabe_758
Callithrix jacchus	retro_cjac_869

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005969	1 retrocopy	retro_amel_1184,
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,
Gorilla gorilla	ENSGGOG00000000041	1 retrocopy	retro_ggor_1955,
Gorilla gorilla	ENSGGOG00000024063	3 retrocopies	retro_ggor_2887, retro_ggor_3019, retro_ggor_330,
Gorilla gorilla	ENSGGOG00000025853	6 retrocopies	retro_ggor_1928, retro_ggor_2281, retro_ggor_2466, retro_ggor_2467, retro_ggor_635 , retro_ggor_845,
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,
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,
Ictidomys tridecemlineatus	ENSSTOG00000006223	4 retrocopies	retro_itri_1093, retro_itri_1682, retro_itri_1764, retro_itri_912,