RetrogeneDB ID: retro_ggor_1104

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 14:48760718..48760942(-)
• Located in intron of: ENSGGOG00000005620

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX7A2
• Ensembl ID: ENSGGOG00000005865
• Aliases: None
• Description: None

Sequence

>retro_ggor_1104
CTGTGGAGTTGTCAGGGTTCATGGGCAGTAACTGAGTCAAGATGCTGCAGAATCTGCTGGCACTGTCAGGTTGCCCAGAG
GACCATGAGCATTGCTTCATGCAGGCATTTTGAAAATAAAGGTCCAGAAAACACAAGCTGTTTCAGGAGAAGAATGGAAT
TCCAGTGCATCTAAAGGGTGGTAGAGCTGATGACCTCCTGTATAGAGCCACCATGGTTCTCAGT

Alignment

ORF - retro_ggor_1104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.26 %
• Parental protein coverage: 65.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VFSCGGCWSVTPKMLRNLLALRQIGQRTISTASRRHFKNKVPE-KQKLFQEDDEIPLYLKGGIADALLYR
          ..SC.G.W.VT...........Q..QRT.S.AS.RHF.NK.PE.K.KLFQE...IP..LKGG.AD.LLYR
Retrocopy LWSCQGSWAVTESRCCRICWHCQVAQRTMSIASCRHFENKGPE<KHKLFQEKNGIPVHLKGGRADDLLYR

Parental  ATMILT
          ATM.L.
Retrocopy ATMVLS

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	0.05 RPM	53.85 RPM
SRP007412_cerebellum	0.12 RPM	36.96 RPM
SRP007412_heart	0.03 RPM	64.45 RPM
SRP007412_kidney	0.12 RPM	92.16 RPM
SRP007412_liver	0.13 RPM	39.57 RPM
SRP007412_testis	0.00 RPM	116.55 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_1104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1104 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1434
Pongo abelii	retro_pabe_1187

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014453	1 retrocopy	retro_amel_723,
Bos taurus	ENSBTAG00000005096	6 retrocopies	retro_btau_1071, retro_btau_1230, retro_btau_1436, retro_btau_1469, retro_btau_1703, retro_btau_507,
Callithrix jacchus	ENSCJAG00000010305	2 retrocopies	retro_cjac_1523, retro_cjac_4129,
Cavia porcellus	ENSCPOG00000007404	2 retrocopies	retro_cpor_1300, retro_cpor_527,
Dipodomys ordii	ENSDORG00000015425	2 retrocopies	retro_dord_701, retro_dord_790,
Homo sapiens	ENSG00000112695	2 retrocopies	retro_hsap_1434, retro_hsap_2961,
Gorilla gorilla	ENSGGOG00000005865	2 retrocopies	retro_ggor_1104 , retro_ggor_2051,
Gorilla gorilla	ENSGGOG00000010739	1 retrocopy	retro_ggor_674,
Loxodonta africana	ENSLAFG00000002313	1 retrocopy	retro_lafr_811,
Microcebus murinus	ENSMICG00000015747	3 retrocopies	retro_mmur_381, retro_mmur_548, retro_mmur_799,
Nomascus leucogenys	ENSNLEG00000004949	2 retrocopies	retro_nleu_1412, retro_nleu_735,
Pongo abelii	ENSPPYG00000016781	2 retrocopies	retro_pabe_1187, retro_pabe_2456,
Pteropus vampyrus	ENSPVAG00000010401	6 retrocopies	retro_pvam_1144, retro_pvam_1408, retro_pvam_443, retro_pvam_57, retro_pvam_656, retro_pvam_741,
Rattus norvegicus	ENSRNOG00000042903	1 retrocopy	retro_rnor_52,
Sus scrofa	ENSSSCG00000004480	1 retrocopy	retro_sscr_296,
Ictidomys tridecemlineatus	ENSSTOG00000002536	5 retrocopies	retro_itri_435, retro_itri_464, retro_itri_608, retro_itri_890, retro_itri_892,
Tupaia belangeri	ENSTBEG00000007294	7 retrocopies	retro_tbel_1177, retro_tbel_178, retro_tbel_3617, retro_tbel_4102, retro_tbel_4330, retro_tbel_738, retro_tbel_781,
Tursiops truncatus	ENSTTRG00000007874	1 retrocopy	retro_ttru_669,