RetrogeneDB ID: retro_ggor_1871

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:99171495..99172190(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000024100
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VTI1B
• Ensembl ID: ENSGGOG00000005620
• Aliases: None
• Description: None

Sequence

>retro_ggor_1871
ATGGCCACCTTCACCGCCTCCTTAGAGCATTTCGAGAAGCTGTACGAGATCTTCCGCGGCCTCCATGAAGACCTACAAGG
GGTGCCCGAGCGGCTGCTGGGGGCGGCGGGGACCGAAGAGAAGAAGTTAATTAGGGATTTTGATGAAAAGCAACAGGAAG
CAAATGAAACTTTGGCAGAGATGGAGGAGGAGCTACGTTATGCACCCCTGTCTTTCTGTAACCCCATGATGTCTAAGCTT
CGAAAACTACCAAAAGGACCTTGCCAAACTCCATCGGGAGGTGAGAAGCACACGTTTGACAGCCACACCTGGAGGCCTAG
GAGACATGAAATATGGCATATATGCTGTAGAGACTGAGCATATGAATCGGCTTACAGTCTCAAAGGGCAACGCTTCCGCA
AGGCACTGAAAGCCTGAAACAGGCCACCCAAAGTATTGAACGTTCTCATCAGACTGCCACGGAGACTGACCAGATTGGCT
CAGAAATCATAGAAGAGCTGGGAGAACAACGAGACCAGTTAGAACGCACCAAGAGTAGACTGGTAAACACAAGTGAAAAC
TTGAGCAACAGTCGAAAGATTCTCCGTTCAATGTCCAGAAAAGTGACAACCAACAAGCTGCTGCTTTCCATCATCATCTT
ACTGGAGCTTGCCATCCTGGGAGGCCTGGTTTACTACAAATTCTTTCGCAAACAT

Alignment

ORF - retro_ggor_1871 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASSAASSEHFEKLHEIFRGLHEDLQGVPERLLGTAGTEKKKKTILLFQKEEQEKPSQLAEMEEELRYAP
          MA...AS.EHFEKL.EIFRGLHEDLQGVPERLLG.AGTE.KK..I..F....QE....LAEMEEELRYAP
Retrocopy MATFTASLEHFEKLYEIFRGLHEDLQGVPERLLGAAGTEEKK-LIRDFDEKQQEANETLAEMEEELRYAP

Parental  LSFRNPMMSKLRK-YRKDLAKLHREVRSTPLTATPGGRGDMKYGIYAVENEHMNRL-QSQRAVLLQGTES
          LSF.NPMMSKLRK.Y.KDLAKLHREVRST.LTATPGG.GDMKYGIYAVE.EHMNRL.QSQRA.L.QGTES
Retrocopy LSFCNPMMSKLRK>YQKDLAKLHREVRSTRLTATPGGLGDMKYGIYAVETEHMNRL>QSQRATLPQGTES

Parental  LNRATQSIERSHRIATETDQIGSEIIEELGEQRDQLERTKSRLVNTSENLSKSRKILRSMSRKVTTNKLL
          L..ATQSIERSH..ATETDQIGSEIIEELGEQRDQLERTKSRLVNTSENLS.SRKILRSMSRKVTTNKLL
Retrocopy LKQATQSIERSHQTATETDQIGSEIIEELGEQRDQLERTKSRLVNTSENLSNSRKILRSMSRKVTTNKLL

Parental  LSIIILLELAILGGLVYYKFFRSH
          LSIIILLELAILGGLVYYKFFR.H
Retrocopy LSIIILLELAILGGLVYYKFFRKH

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	5.27 RPM	45.12 RPM
SRP007412_cerebellum	2.29 RPM	21.51 RPM
SRP007412_heart	1.44 RPM	14.13 RPM
SRP007412_kidney	5.93 RPM	53.16 RPM
SRP007412_liver	1.42 RPM	16.06 RPM
SRP007412_testis	6.63 RPM	39.06 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_1871 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1871 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2682
Pongo abelii	retro_pabe_2298
Macaca mulatta	retro_mmul_1420

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015263	1 retrocopy	retro_cjac_1439,
Dasypus novemcinctus	ENSDNOG00000003643	2 retrocopies	retro_dnov_1503, retro_dnov_2031,
Dipodomys ordii	ENSDORG00000015939	2 retrocopies	retro_dord_52, retro_dord_716,
Echinops telfairi	ENSETEG00000006101	1 retrocopy	retro_etel_783,
Felis catus	ENSFCAG00000014090	1 retrocopy	retro_fcat_1855,
Homo sapiens	ENSG00000100568	3 retrocopies	retro_hsap_1002, retro_hsap_2682, retro_hsap_3013,
Gorilla gorilla	ENSGGOG00000005620	2 retrocopies	retro_ggor_1871 , retro_ggor_797,
Macropus eugenii	ENSMEUG00000004910	2 retrocopies	retro_meug_499, retro_meug_697,
Microcebus murinus	ENSMICG00000010843	1 retrocopy	retro_mmur_849,
Myotis lucifugus	ENSMLUG00000011184	3 retrocopies	retro_mluc_1299, retro_mluc_2393, retro_mluc_781,
Macaca mulatta	ENSMMUG00000015866	1 retrocopy	retro_mmul_1420,
Mustela putorius furo	ENSMPUG00000007130	1 retrocopy	retro_mputfur_1516,
Nomascus leucogenys	ENSNLEG00000000780	4 retrocopies	retro_nleu_1184, retro_nleu_2241, retro_nleu_231, retro_nleu_83,
Pongo abelii	ENSPPYG00000005927	5 retrocopies	retro_pabe_2298, retro_pabe_2498, retro_pabe_2602, retro_pabe_845, retro_pabe_974,
Pan troglodytes	ENSPTRG00000006468	3 retrocopies	retro_ptro_1808, retro_ptro_2037, retro_ptro_751,
Pteropus vampyrus	ENSPVAG00000011671	3 retrocopies	retro_pvam_132, retro_pvam_592, retro_pvam_797,
Tupaia belangeri	ENSTBEG00000003049	1 retrocopy	retro_tbel_3432,
Tarsius syrichta	ENSTSYG00000007688	2 retrocopies	retro_tsyr_1662, retro_tsyr_94,