RetrogeneDB ID: retro_ggor_372

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:29089153..29089831(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000023525
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SPCS2
• Ensembl ID: ENSGGOG00000014500
• Aliases: None
• Description: None

Sequence

>retro_ggor_372
ATGGCGGCGGCAGCTGTACAGGGCAGGAGAAGCGGTGGTAGCGGAGGCTGTAGTGGGGCTGGTGGTGCTTCCAACTGCGG
GACAGGAAGTGGCCGTGGCGGCTTGTTGGATAAGTGGAAGATAGATGATAAGCCTGTAAAAATTGACAAGTGGGATGGAT
CAGCTGTGAAAAACTCTTTGGATGATTCTGCCAAAAAGGTACTTCTGGAAAAATATAAATATGTGGAGAATTTTGGTCTA
ATTGATGGTCGCCTCACCATCTGTACAATCTCCTGTTTCTTTGCCATAGTGGCTTTGATTTGGGATTATATGCACCCCTT
TCCAGAGTCCAAACCCGTTTTGGCTTTGTGTGTCATATCCTATTTTGTGATGATGGGGATTCTGACCATTTATACCTCAT
ATAAGGAGAAGAGCATCTTTCTCGTGGCCCACAGGAAAGATCCTACAGGAATGGATCCTGATGATATTTGGCAGCTGTCC
TCCAGTCTTAAAAGGTTTGATGACAAATACACCTTGAAGCTGACCTTCATCAGTGGGAGAACAAAGCAGCAGCGGGAAGC
CGAGTTCACAAAGTCCATTGCTAAGTTTTTTGACCACAGTGGGACACTGGTCATGGATGCATATGAGCCTGAAATATCCA
GGCTCCATGACAGTCTTGCCATAGAAAGAAAAATAAAG

Alignment

ORF - retro_ggor_372 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAAVQGGRSGGSGGCSGAGGASNCGTGSGRSGLLDKWKIDDKPVKIDKWDGSAVKNSLDDSAKKVLLE
          MAAAAVQG.RSGGSGGCSGAGGASNCGTGSGR.GLLDKWKIDDKPVKIDKWDGSAVKNSLDDSAKKVLLE
Retrocopy MAAAAVQGRRSGGSGGCSGAGGASNCGTGSGRGGLLDKWKIDDKPVKIDKWDGSAVKNSLDDSAKKVLLE

Parental  KYKYVENFGLIDGRLTICTISCFFAIVALIWDYMHPFPESKPVLALCVISSYFVMMGILTIYTSYKEKSI
          KYKYVENFGLIDGRLTICTISCFFAIVALIWDYMHPFPESKPVLALCVIS.YFVMMGILTIYTSYKEKSI
Retrocopy KYKYVENFGLIDGRLTICTISCFFAIVALIWDYMHPFPESKPVLALCVIS-YFVMMGILTIYTSYKEKSI

Parental  FLVAHRKDPTGMDPDDIWQLSSSLKRFDDKYTLKLTFISGRTKQQREAEFTKSIAKFFDHSGTLVMDAYE
          FLVAHRKDPTGMDPDDIWQLSSSLKRFDDKYTLKLTFISGRTKQQREAEFTKSIAKFFDHSGTLVMDAYE
Retrocopy FLVAHRKDPTGMDPDDIWQLSSSLKRFDDKYTLKLTFISGRTKQQREAEFTKSIAKFFDHSGTLVMDAYE

Parental  PEISRLHDSLAIERKIK
          PEISRLHDSLAIERKIK
Retrocopy PEISRLHDSLAIERKIK

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	1.39 RPM	22.87 RPM
SRP007412_cerebellum	1.65 RPM	14.26 RPM
SRP007412_heart	0.50 RPM	7.50 RPM
SRP007412_kidney	3.35 RPM	9.85 RPM
SRP007412_liver	2.40 RPM	9.18 RPM
SRP007412_testis	2.38 RPM	20.82 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_372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_372 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_360

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017127	1 retrocopy	retro_amel_1372,
Choloepus hoffmanni	ENSCHOG00000002974	3 retrocopies	retro_chof_1392, retro_chof_1588, retro_chof_2300,
Callithrix jacchus	ENSCJAG00000015576	2 retrocopies	retro_cjac_1500, retro_cjac_1929,
Cavia porcellus	ENSCPOG00000007273	2 retrocopies	retro_cpor_438, retro_cpor_578,
Dipodomys ordii	ENSDORG00000009679	1 retrocopy	retro_dord_423,
Homo sapiens	ENSG00000118363	4 retrocopies	retro_hsap_1488, retro_hsap_3137, retro_hsap_360, retro_hsap_723,
Gorilla gorilla	ENSGGOG00000014500	3 retrocopies	retro_ggor_1141, retro_ggor_372 , retro_ggor_610,
Microcebus murinus	ENSMICG00000011153	2 retrocopies	retro_mmur_1566, retro_mmur_656,
Macaca mulatta	ENSMMUG00000010685	1 retrocopy	retro_mmul_26,
Monodelphis domestica	ENSMODG00000007130	2 retrocopies	retro_mdom_1127, retro_mdom_1454,
Mus musculus	ENSMUSG00000035227	1 retrocopy	retro_mmus_2088,
Nomascus leucogenys	ENSNLEG00000016949	2 retrocopies	retro_nleu_1710, retro_nleu_470,
Otolemur garnettii	ENSOGAG00000015621	1 retrocopy	retro_ogar_2649,
Ochotona princeps	ENSOPRG00000014459	2 retrocopies	retro_opri_266, retro_opri_948,
Pongo abelii	ENSPPYG00000003682	4 retrocopies	retro_pabe_1237, retro_pabe_2619, retro_pabe_2817, retro_pabe_625,
Pan troglodytes	ENSPTRG00000004073	1 retrocopy	retro_ptro_1007,
Rattus norvegicus	ENSRNOG00000018164	2 retrocopies	retro_rnor_2078, retro_rnor_2168,
Sarcophilus harrisii	ENSSHAG00000005389	1 retrocopy	retro_shar_787,
Sus scrofa	ENSSSCG00000014850	1 retrocopy	retro_sscr_648,
Ictidomys tridecemlineatus	ENSSTOG00000012647	2 retrocopies	retro_itri_1283, retro_itri_1584,
Tursiops truncatus	ENSTTRG00000005830	3 retrocopies	retro_ttru_1478, retro_ttru_1496, retro_ttru_1867,