RetrogeneDB ID: retro_ggor_899

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 12:107388676..107389206(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000025701
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDCD2
• Ensembl ID: ENSGGOG00000028229
• Aliases: None
• Description: None

Sequence

>retro_ggor_899
CTGGCCTGAGAGCTGTGCGACCGTCGCTCTTCTTCCGGCGGCAGGTGTATGCGTCGCTGCCCGGCCGCGCAGACGCCTTC
CACCGCGGCATCTTCCTCTTCTGCTGCCACGAGCCGCCGTGCTGTGCCGCCCTGCGAGTTTCTAGGAATCAGCTACCCAG
GAAAAATGATTTTTACTCATATGAGCCACCTTCTGAGACTCCTTCCCCAGAAACAGGAGAATCGGTGTATCTCCAACTTA
AGTCTGGTGCTCATCTCTGCAGGGTTTGTGGCTGTTTAGGCCCCAAAACTTGCTCCAGATGCCACAAAGCGTATTACTGC
AGCAAGGAGCATCAGACCCTAGACTGGAGATTGGGACATAAGCAGGCTTGTGCACAACCAGATCATTTGGACCTTACAAC
TCCAGACCACAGCTTCCTTTTTCCAGAATTTGAAATTGTAATAGGAACAGAAGACGAGATTATGCCTGAGGTTGCGGAAA
AGGAAGATTATTCAGATATTATAGGGAGCATGGTTAAGCAGTTTCAGGAC

Alignment

ORF - retro_ggor_899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.15 %
• Parental protein coverage: 51.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LACELCGR-PLSFLLQVYAPLPGRPDAFHRCIFLFCCREQPCCAGLRVFRNQLPRKNDFYSYEPPSENPP
          LA.ELC.R..L.F..QVYA.LPGR.DAFHR.IFLFCC.E.PCCA.LRV.RNQLPRKNDFYSYEPPSE.P.
Retrocopy LA*ELCDR<SLFFRRQVYASLPGRADAFHRGIFLFCCHEPPCCAALRVSRNQLPRKNDFYSYEPPSETPS

Parental  PETGESVCLQLKSGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQTLDWRLGHKQACAQPDHLDHIIPDHNF
          PETGESV.LQLKSGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQTLDWRLGHKQACAQPDHLD...PDH.F
Retrocopy PETGESVYLQLKSGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQTLDWRLGHKQACAQPDHLDLTTPDHSF

Parental  LFPEFEIVIETEDEIMPEVVEKEDYSEIIGSMGEALEE
          LFPEFEIVI.TEDEIMPEV.EKEDYS.IIGSM......
Retrocopy LFPEFEIVIGTEDEIMPEVAEKEDYSDIIGSMVKQFQD

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	7.48 RPM
SRP007412_cerebellum	0.00 RPM	8.08 RPM
SRP007412_heart	0.00 RPM	4.07 RPM
SRP007412_kidney	0.00 RPM	16.44 RPM
SRP007412_liver	0.00 RPM	11.98 RPM
SRP007412_testis	0.10 RPM	7.87 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_899 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_899 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_788
Pongo abelii	retro_pabe_958

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017075	2 retrocopies	retro_amel_1329, retro_amel_1404,
Callithrix jacchus	ENSCJAG00000020634	1 retrocopy	retro_cjac_3946,
Equus caballus	ENSECAG00000016819	1 retrocopy	retro_ecab_533,
Felis catus	ENSFCAG00000007037	2 retrocopies	retro_fcat_305, retro_fcat_749,
Homo sapiens	ENSG00000071994	1 retrocopy	retro_hsap_4305,
Gorilla gorilla	ENSGGOG00000028229	2 retrocopies	retro_ggor_2876, retro_ggor_899 ,
Microcebus murinus	ENSMICG00000007474	1 retrocopy	retro_mmur_108,
Macaca mulatta	ENSMMUG00000019916	1 retrocopy	retro_mmul_1137,
Mustela putorius furo	ENSMPUG00000007227	2 retrocopies	retro_mputfur_621, retro_mputfur_707,
Nomascus leucogenys	ENSNLEG00000000295	2 retrocopies	retro_nleu_1458, retro_nleu_2633,
Otolemur garnettii	ENSOGAG00000014002	2 retrocopies	retro_ogar_2090, retro_ogar_2288,
Pongo abelii	ENSPPYG00000017193	2 retrocopies	retro_pabe_3505, retro_pabe_958,
Pan troglodytes	ENSPTRG00000018828	2 retrocopies	retro_ptro_2915, retro_ptro_788,
Pteropus vampyrus	ENSPVAG00000010822	1 retrocopy	retro_pvam_1150,
Sus scrofa	ENSSSCG00000025312	2 retrocopies	retro_sscr_303, retro_sscr_450,