RetrogeneDB ID: retro_ggor_2203

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:113941086..113941458(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXN
• Ensembl ID: ENSGGOG00000007636
• Aliases: None
• Description: None

Sequence

>retro_ggor_2203
GTCCATTTCATGAATCTGAAGAAAATGGTAACTTGGTGTGGCCAAAGCTCTCTAGGTAAGGCCACCTATAAACGACTGGC
AGAGGAGATGACAAATTTGTTAGTAGATTGGCTATTTGTTTTTTGAAAGCTTGCAAACAAATCGTACACAGTTGAGATTT
AAGATGTCTAATTTTGGGAGTAGTATTTTAGTAATTAAACTGTGTGGAGATAGAGGAGCCTACAGGATGAACAAGCAAAC
CCCAAATAAGTAAATCTTGTTCTCACTTCCATCTAATGGACCCAAGCATTATGATTGGAATGGGAACAACTGGATCTATT
CCCACAACAAGGGTGTACCTCTCCACAAACTGCTATCCCAGAGCTGACTAAA

Alignment

ORF - retro_ggor_2203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.97 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VYLMNLRKSGTLGHPGSLDETTYERLAEETLDSLAEF---FEDLADKPYTFEDYDV-SFGSGVLTVKLGG
          V..MNL.K..T.....SL...TY.RLAEE....L......F..LA.K.YT.E..DV..FGS..L..KL.G
Retrocopy VHFMNLKKMVTWCGQSSLGKATYKRLAEEMTNLLVDWLFVF*KLANKSYTVEI*DV>NFGSSILVIKLCG

Parental  DLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHD-GVSLHELLA-AELTK
          D.G.Y..NKQTPNK.I..S.PS.GPK.YDW.G.NW.YSH..GV.LH.LL...ELTK
Retrocopy DRGAYRMNKQTPNK*ILFSLPSNGPKHYDWNGNNWIYSHNKGVPLHKLLS<PELTK

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	5.90 RPM
SRP007412_cerebellum	0.00 RPM	4.73 RPM
SRP007412_heart	0.00 RPM	3.53 RPM
SRP007412_kidney	0.00 RPM	5.77 RPM
SRP007412_liver	0.00 RPM	5.54 RPM
SRP007412_testis	0.00 RPM	5.28 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_2203 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2203 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2038
Equus caballus	retro_ecab_311

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006915	1 retrocopy	retro_amel_1496,
Choloepus hoffmanni	ENSCHOG00000005107	2 retrocopies	retro_chof_349, retro_chof_94,
Callithrix jacchus	ENSCJAG00000001695	4 retrocopies	retro_cjac_1562, retro_cjac_1927, retro_cjac_3939, retro_cjac_813,
Dasypus novemcinctus	ENSDNOG00000024066	3 retrocopies	retro_dnov_2204, retro_dnov_2317, retro_dnov_307,
Equus caballus	ENSECAG00000019174	1 retrocopy	retro_ecab_311,
Homo sapiens	ENSG00000165060	2 retrocopies	retro_hsap_1447, retro_hsap_4311,
Gorilla gorilla	ENSGGOG00000007636	3 retrocopies	retro_ggor_1112, retro_ggor_2203 , retro_ggor_2881,
Macaca mulatta	ENSMMUG00000000357	2 retrocopies	retro_mmul_2038, retro_mmul_826,
Mustela putorius furo	ENSMPUG00000009619	2 retrocopies	retro_mputfur_501, retro_mputfur_803,
Mus musculus	ENSMUSG00000059363	2 retrocopies	retro_mmus_1571, retro_mmus_3058,
Otolemur garnettii	ENSOGAG00000031105	2 retrocopies	retro_ogar_1865, retro_ogar_476,
Rattus norvegicus	ENSRNOG00000015213	1 retrocopy	retro_rnor_2276,
Tursiops truncatus	ENSTTRG00000010336	4 retrocopies	retro_ttru_1281, retro_ttru_175, retro_ttru_546, retro_ttru_831,