RetrogeneDB ID: retro_ggor_2396

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:5129978..5130530(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000026019
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TFB2M
• Ensembl ID: ENSGGOG00000001095
• Aliases: None
• Description: None

Sequence

>retro_ggor_2396
TGGATCCCAGTGGCCAGATTTCCTCCTCGGCTGAGGCTCTCCGCCTTGGGGGGTGCTGGTCACTTTTGCATTTTAGGGTC
TGGAGCGGCGACGCGAAAGCACTTGCCAGCGAGGAACCGCCGTGGCCTGTCTGACTCCTCTCCGCAGCTGTGGCCGGATC
CGGATTTCAAGAACTCACCAAGGAGGGTGTTAAACTCCATCTTAGACTTTAAGCGTTACGTAACCAATCGGAGATTGGCT
GAGACCCTGGCGCAAATCGTATGGAGAAAACAAAATAGACCTCCACACCTATTGCTGCAGTGCAGTCCAGATCCTGGAAT
CCTGACTCAGGCATTACTTGAAATTGGTGCCAAAGTGGTTGCCCTTGAAAGTGACAAAACTTTTATTCCACATTTGGAGT
CCTTAGGAAAAAATCTGGATGGAAAACTACAAGTGATTCACTGTGACTTCTTTAAAATAGATCCTAGAAGTGGTGGAGTA
ATAAAGCCACCCGCTATGGCTTCTCACGGGCTCTTTCAGAATTTGGGAATAGAAGCAGTTCCTTGGACAGCA

Alignment

ORF - retro_ggor_2396 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.98 %
• Parental protein coverage: 53.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WIPVVGLPRRLRLSALAGAGRFCILGSEAATRKHLPARNHCGLSDSSPQLWPEPDFRNPPRKASKARLDY
          WIPV...P.RLRLSAL.GAG.FCILGS.AATRKHLPARN..GLSDSSPQLWP.PDF.N.PR......LD.
Retrocopy WIPVARFPPRLRLSALGGAGHFCILGSGAATRKHLPARNRRGLSDSSPQLWPDPDFKNSPRRVLNSILDF

Parental  KRYVTDRRLAETLAQIYLGKPSRPPHLLLECNPGPGILTQALLEAGAKVVALESDKTFIPHLESLGKNLD
          KRYVT.RRLAETLAQI...K..RPPHLLL.C.P.PGILTQALLE.GAKVVALESDKTFIPHLESLGKNLD
Retrocopy KRYVTNRRLAETLAQIVWRKQNRPPHLLLQCSPDPGILTQALLEIGAKVVALESDKTFIPHLESLGKNLD

Parental  GRLRVIHCDFFKLDPRSGGVIKPPAMSSRGLFKNLGIEAVPWTA
          G.L.VIHCDFFK.DPRSGGVIKPPAM.S.GLF.NLGIEAVPWTA
Retrocopy GKLQVIHCDFFKIDPRSGGVIKPPAMASHGLFQNLGIEAVPWTA

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	0.62 RPM	4.60 RPM
SRP007412_cerebellum	0.20 RPM	3.70 RPM
SRP007412_heart	0.03 RPM	1.78 RPM
SRP007412_kidney	0.04 RPM	10.47 RPM
SRP007412_liver	0.03 RPM	18.20 RPM
SRP007412_testis	0.00 RPM	9.53 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_2396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2396 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013225	1 retrocopy	retro_cpor_451,
Homo sapiens	ENSG00000162851	1 retrocopy	retro_hsap_3548,
Gorilla gorilla	ENSGGOG00000001095	1 retrocopy	retro_ggor_2396 ,
Myotis lucifugus	ENSMLUG00000003923	1 retrocopy	retro_mluc_1302,
Macaca mulatta	ENSMMUG00000022915	1 retrocopy	retro_mmul_1814,
Nomascus leucogenys	ENSNLEG00000004146	1 retrocopy	retro_nleu_2323,
Oryctolagus cuniculus	ENSOCUG00000013727	2 retrocopies	retro_ocun_1557, retro_ocun_236,
Otolemur garnettii	ENSOGAG00000007823	2 retrocopies	retro_ogar_1444, retro_ogar_2187,
Pongo abelii	ENSPPYG00000000046	1 retrocopy	retro_pabe_3039,
Pan troglodytes	ENSPTRG00000002188	1 retrocopy	retro_ptro_2412,