RetrogeneDB ID: retro_ggor_536

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 10:105250534..105250870(+)
• Located in intron of: ENSGGOG00000016441

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDHC
• Ensembl ID: ENSGGOG00000008017
• Aliases: None
• Description: None

Sequence

>retro_ggor_536
ATCTACAGTTGGTCTCTTCCCATGGCGATGGCCATCTGCCACCGTGACACTGGTACTGCTTTGAGGGCAGGGGCCTCTCT
TTTTGGCATGTCAGCCCTGTTACTCCCTGGGAACTTTGAGTCTTATTTGGAGCTCGTGAAGTCCCTGTGTCTGGGGCCAG
CACTGATCCACACAGCTAAGTTTGCACTCGTCTTCCCTCTCATGTATCATACCTGGAATGGGGTCTGACACTTGATGTGG
GACCTAGGAAAAGGCCTGAAGATTCCCCAGCTATACCAGTCTGGAGTGGCTGTCCTGGTTCTTACTGTGTTGTCCTCTGT
AGGGCTGGCAGCCATA

Alignment

ORF - retro_ggor_536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.29 %
• Parental protein coverage: 96.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLSWSLPMAMSICHRGTGIALSAGVSLFGMSALLLPGNFESYLELLKSLCLGPALIHTAKFALVFPLMYH
          ..SWSLPMAM.ICHR.TG.AL.AG.SLFGMSALLLPGNFESYLEL.KSLCLGPALIHTAKFALVFPLMYH
Retrocopy IYSWSLPMAMAICHRDTGTALRAGASLFGMSALLLPGNFESYLELVKSLCLGPALIHTAKFALVFPLMYH

Parental  TWNGIRHLMWDLGKGLKIPQLYQSGVVVLVLTVLSSVGLAAM
          TWNG..HLMWDLGKGLKIPQLYQSGV.VLVLTVLSSVGLAA.
Retrocopy TWNGV*HLMWDLGKGLKIPQLYQSGVAVLVLTVLSSVGLAAI

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	0.19 RPM	12.18 RPM
SRP007412_cerebellum	0.00 RPM	8.08 RPM
SRP007412_heart	0.09 RPM	12.16 RPM
SRP007412_kidney	0.20 RPM	35.12 RPM
SRP007412_liver	0.21 RPM	18.94 RPM
SRP007412_testis	0.21 RPM	12.12 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_536 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_536 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_609
Macaca mulatta	retro_mmul_2416
Callithrix jacchus	retro_cjac_988

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015351	2 retrocopies	retro_amel_468, retro_amel_803,
Bos taurus	ENSBTAG00000015853	1 retrocopy	retro_btau_835,
Canis familiaris	ENSCAFG00000012992	2 retrocopies	retro_cfam_1529, retro_cfam_275,
Callithrix jacchus	ENSCJAG00000004757	3 retrocopies	retro_cjac_1119, retro_cjac_2455, retro_cjac_988,
Echinops telfairi	ENSETEG00000015767	1 retrocopy	retro_etel_675,
Felis catus	ENSFCAG00000000499	1 retrocopy	retro_fcat_1609,
Homo sapiens	ENSG00000143252	4 retrocopies	retro_hsap_1794, retro_hsap_1896, retro_hsap_609, retro_hsap_854,
Gorilla gorilla	ENSGGOG00000008017	3 retrocopies	retro_ggor_1390, retro_ggor_536 , retro_ggor_697,
Macaca mulatta	ENSMMUG00000012411	11 retrocopies	retro_mmul_1063, retro_mmul_1323, retro_mmul_1338, retro_mmul_1686, retro_mmul_1845, retro_mmul_2002, retro_mmul_2087, retro_mmul_239, retro_mmul_2416, retro_mmul_369, retro_mmul_672,
Mustela putorius furo	ENSMPUG00000014439	1 retrocopy	retro_mputfur_1201,
Nomascus leucogenys	ENSNLEG00000014367	3 retrocopies	retro_nleu_1476, retro_nleu_420, retro_nleu_439,
Pteropus vampyrus	ENSPVAG00000005544	2 retrocopies	retro_pvam_879, retro_pvam_974,
Rattus norvegicus	ENSRNOG00000003163	2 retrocopies	retro_rnor_1486, retro_rnor_1487,
Sarcophilus harrisii	ENSSHAG00000016835	1 retrocopy	retro_shar_205,
Sus scrofa	ENSSSCG00000030318	2 retrocopies	retro_sscr_1050, retro_sscr_1061,
Takifugu rubripes	ENSTRUG00000001873	1 retrocopy	retro_trub_41,
Tursiops truncatus	ENSTTRG00000009234	1 retrocopy	retro_ttru_196,