RetrogeneDB ID: retro_ggor_1955

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:90275563..90275985(-)
• Located in intron of: ENSGGOG00000000500

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX5
• Ensembl ID: ENSGGOG00000000041
• Aliases: None
• Description: None

Sequence

>retro_ggor_1955
ATGGGAAAGAAAACCAAGCACACAGCTAACAGTTCATCAGAGAATGAAGAGGAGTACACTGTGGAGAAGGTGCTAGACAG
GCATGTGGTTAAGGGGCAAGTGGAGTATCTGCTGAAGTGGAAAGGCTTTTCTGAGGAGCACAATACTTGGGAATCTGAGA
AAAACTTGGATTGCCTTTAGCTCATTTCTTAGTTTACAAAAAAGTTTAAGATGATGAAGGAGGGTTAAAATAACAAGCCT
GGCGAGAAGTCACAAAGTAGCAAAGAAATCCAATTTCTCAAACTGTGCTGACAGTATCAAGTCCAAAAAAGAGAACAGAG
TGATGATATTGCTTGGGGCTTCGAGATAAGACTAGAACCAGAAAAGATCATTGGGGCAACAGATTCCTGTGGCAATTTAT
GTTTTTAATGAAATGGAAAGAC

Alignment

ORF - retro_ggor_1955 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.VVKGQVEYLLKWKGFSEEHNTWE.EKNLDC..LIS.F.KK.
Retrocopy MGKKTKHTANSSS-ENEEEYTVEKVLDRHVVKGQVEYLLKWKGFSEEHNTWESEKNLDCL*LIS*FTKKF

Parental  KKMKEGENNKPREKSESNKRKSNFSNSADDIKSKKKREQSNDIARGFERGLEPEKIIGATDSCGDL-MFL
          K.MKEG.NNKP.EKS.S.K....F..........K.......IA.GFE..LEPEKIIGATDSCG.L.MFL
Retrocopy KMMKEG*NNKPGEKSQSSK-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	0.14 RPM	19.28 RPM
SRP007412_cerebellum	0.08 RPM	19.86 RPM
SRP007412_heart	0.00 RPM	5.72 RPM
SRP007412_kidney	0.00 RPM	14.88 RPM
SRP007412_liver	0.00 RPM	3.48 RPM
SRP007412_testis	0.10 RPM	85.68 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_1955 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1955 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2811
Pan troglodytes	retro_ptro_1905
Pongo abelii	retro_pabe_2307

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 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 ,
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,
Nomascus leucogenys	ENSNLEG00000017671	1 retrocopy	retro_nleu_428,
Pongo abelii	ENSPPYG00000004599	1 retrocopy	retro_pabe_2307,
Pan troglodytes	ENSPTRG00000005034	1 retrocopy	retro_ptro_1905,
Tursiops truncatus	ENSTTRG00000004524	1 retrocopy	retro_ttru_1859,