RetrogeneDB ID: retro_ggor_648

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 11:53221403..53221903(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCHL1
• Ensembl ID: ENSGGOG00000008809
• Aliases: None
• Description: None

Sequence

>retro_ggor_648
TGCCAGCACCTGCCTACTCTTTGTATCAGAGCCTCACACAAGAACCTCAGGAAAAATTGATTGAAGAACTGAAGAGACAA
GGAGATAGTCCTAAAGGGTACTTCATGAAGCAGAGTATCGGAAACTTCTGTCACACAATTAGACTTATACATGCAATGGC
CAATAACCAAGACAAACTAAAATTCGAGGCAGGTCAATCCTGAAATATTTTATTTCTGACATGGAGAAAAATATCACCTG
AAGACAGCACAAAATCCTTTGAAAATAATAAGGCCTTTCAGGCAGTTTATGAGGCTATCTTATAGCAAAGCCAATGTCAG
GCAGATGACAAAGTGAATTTTTGTTTTATTCTGTTTAGCAATGCGGATGGCCACCTCTCTGAACTTGGTGGATGAGTGCC
TTTCCTAGTGAACTATGGTGCCAGTTCAGAGGACTCACTGCTGCAGGATTGTAGTGATTAGGCTGCCAAGGTCTGCATGA
AATTTACTAAGGAGGAAGAA

Alignment

ORF - retro_ggor_648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 73.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CALLLLFPLTAQHENFRK-KQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDG-SVL
          C..L......A.H.N.RK.K.IEELK.Q..SPK.YFMKQ.IGN.C.TI.LIHA.ANNQDKL.FE.G.S.L
Retrocopy CQHLPTLCIRASHKNLRK<KLIEELKRQGDSPKGYFMKQSIGNFCHTIRLIHAMANNQDKLKFEAG<SIL

Parental  KQFLSETE-KMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGRMPFPV
          K.F.S..E.K.SPED..K.FE.N.A.QA...A.....QC..DDKVNF.FILF.N.DGHL.EL.G..PF.V
Retrocopy KYFISDME>KISPEDSTKSFENNKAFQAVYEAIL*QSQCQADDKVNFCFILFSNADGHLSELGG*VPFLV

Parental  NHGASSEDTLLKD----AAKVCREFTEREQ
          N.GASSED.LL.D....AAKVC..FT..E.
Retrocopy NYGASSEDSLLQDCSD*AAKVCMKFTKEEE

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	911.80 RPM
SRP007412_cerebellum	0.00 RPM	105.35 RPM
SRP007412_heart	0.00 RPM	2.94 RPM
SRP007412_kidney	0.00 RPM	16.64 RPM
SRP007412_liver	0.00 RPM	0.76 RPM
SRP007412_testis	0.00 RPM	30.35 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_648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_648 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019346	1 retrocopy	retro_cjac_365,
Erinaceus europaeus	ENSEEUG00000002185	3 retrocopies	retro_eeur_150, retro_eeur_573, retro_eeur_598,
Echinops telfairi	ENSETEG00000012347	1 retrocopy	retro_etel_44,
Homo sapiens	ENSG00000154277	2 retrocopies	retro_hsap_781, retro_hsap_782,
Gorilla gorilla	ENSGGOG00000008809	1 retrocopy	retro_ggor_648 ,
Macropus eugenii	ENSMEUG00000013774	1 retrocopy	retro_meug_8,
Myotis lucifugus	ENSMLUG00000010138	2 retrocopies	retro_mluc_1216, retro_mluc_2113,
Nomascus leucogenys	ENSNLEG00000017176	2 retrocopies	retro_nleu_2582, retro_nleu_2583,
Oryctolagus cuniculus	ENSOCUG00000001353	1 retrocopy	retro_ocun_309,
Pan troglodytes	ENSPTRG00000016009	2 retrocopies	retro_ptro_3028, retro_ptro_3029,
Tarsius syrichta	ENSTSYG00000008305	1 retrocopy	retro_tsyr_1191,