RetrogeneDB ID: retro_ggor_2711

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:37947414..37948080(-)
• Located in intron of: ENSGGOG00000012855

Retrocopy information

• Ensembl ID: ENSGGOG00000028204
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CXORF56
• Ensembl ID: ENSGGOG00000013324
• Aliases: None
• Description: None

Sequence

>retro_ggor_2711
ATGCCGAAAGTAGTGTCTCGGTCAGTAGTCTGCTCTGACACTCGGGACCGGGAGGAATATGACGACGGCGAGAAGCCCCT
CCATGTGTACTACTGTTTGTGTGGCCAGGTGGTCCTAGTGCTGGACTGTCAGTTAGAGAAATTGCCCATGAGGCCCCGGG
ACCGGTCCCGTGTGATTGATGCTGCCAAACATACCCATAAGTTTTGTAACACAGAAGACGAAGAGACTATGTATCTGCGG
AGACCTGAAGGCATTGAACTACAGTACAGAAAGAAATGTGCAAAGTGTGGACTGCTGCTCTTCTACCAATCCCAGCCGAA
GAATGCTCCCGTTACCTTCATTGTGGATGGAGCAGTAGTCAAGTTTGGCCAGGGCTTTGGGAAAACGAACATATATACTC
AGAAACAAGAGCCTCCTAAGAAGGTGATGATGACCAAACGGACCAAAGACATGGGCAAGTTCAGTTCTGTCACTGTGTCT
ACCATTGATGAAGAGGAAGAGGAGATTGAGGCTAGGGAAGTTGCTGACTCGTATGCACAGAATGCCAAAGTGATTGAAAA
ACAGCTGGAGCGCAAAGGCATGAGCAAGAGGCCACTGCAAGAGCTGGCTGAATGGGAAGCCAAGAAAGTGAAAATGAAGG
GGACCTTGATTGACAACCAGTTCAAA

Alignment

ORF - retro_ggor_2711 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.85 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGQMVLVLDCQLEKLPMRPRDRSRVIDAAKHAHKFCN
          MPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGQ.VLVLDCQLEKLPMRPRDRSRVIDAAKH.HKFCN
Retrocopy MPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGQVVLVLDCQLEKLPMRPRDRSRVIDAAKHTHKFCN

Parental  TEDEETMYLRRPEGIERQYRKKCAKCGLPLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK
          TEDEETMYLRRPEGIE.QYRKKCAKCGL.LFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK
Retrocopy TEDEETMYLRRPEGIELQYRKKCAKCGLLLFYQSQPKNAPVTFIVDGAVVKFGQGFGKTNIYTQKQEPPK

Parental  KVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKRRLQELAELEAKKA
          KVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKR.LQELAE.EAKK.
Retrocopy KVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQNAKVIEKQLERKGMSKRPLQELAEWEAKKV

Parental  KMKGTLIDNQFK
          KMKGTLIDNQFK
Retrocopy KMKGTLIDNQFK

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	0.58 RPM	20.91 RPM
SRP007412_cerebellum	0.63 RPM	12.69 RPM
SRP007412_heart	0.13 RPM	2.91 RPM
SRP007412_kidney	0.25 RPM	14.72 RPM
SRP007412_liver	0.16 RPM	5.09 RPM
SRP007412_testis	5.70 RPM	8.29 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_2711 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2711 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4044
Pan troglodytes	retro_ptro_104
Pongo abelii	retro_pabe_177

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005111	1 retrocopy	retro_cjac_311,
Homo sapiens	ENSG00000018610	1 retrocopy	retro_hsap_4044,
Gorilla gorilla	ENSGGOG00000013324	1 retrocopy	retro_ggor_2711 ,
Latimeria chalumnae	ENSLACG00000012468	1 retrocopy	retro_lcha_59,
Myotis lucifugus	ENSMLUG00000015751	1 retrocopy	retro_mluc_72,
Macaca mulatta	ENSMMUG00000022665	1 retrocopy	retro_mmul_2333,
Mus musculus	ENSMUSG00000006423	1 retrocopy	retro_mmus_1715,
Nomascus leucogenys	ENSNLEG00000014862	1 retrocopy	retro_nleu_2057,
Otolemur garnettii	ENSOGAG00000012474	1 retrocopy	retro_ogar_145,
Pongo abelii	ENSPPYG00000020670	1 retrocopy	retro_pabe_177,
Pan troglodytes	ENSPTRG00000022224	1 retrocopy	retro_ptro_104,
Sorex araneus	ENSSARG00000003163	1 retrocopy	retro_sara_5,
Sarcophilus harrisii	ENSSHAG00000006319	1 retrocopy	retro_shar_16,
Ictidomys tridecemlineatus	ENSSTOG00000011579	1 retrocopy	retro_itri_103,
Tursiops truncatus	ENSTTRG00000013101	2 retrocopies	retro_ttru_231, retro_ttru_77,