RetrogeneDB ID: retro_ggor_2876

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:96396751..96397646(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ggor_2876
CAGACCCTGGCCTGCGCGTTGTGCTGCTGCCAGCTCTCCTTCCTGCTACAGGTGTACGCGCTGCTGCCCGGCCGCGCCGC
CGCCTTCCACCCCGGAATCTTCCTCTTCTGCTGCTGAGAGCCGCCGTGCTGTGCCGGCCTTCGAGTTTTTACCAATCAGC
TACCCAGGAAAAATGATTTTTCCTCATATGGGCCACCTTCTGAGAATCCTCTCCCAGAAACAGGACAATCAGTGTGTCTC
TAACTTAAGTCTGGTGCTCATCTCTGCAGGGTTTGTGGCTGTTTAGGACCCAAAACGTGCTCCAGATGCCACAAAGCGTA
TTACTGCAGCAAGGAGCATCAAGACCCTAGACCGGAGATTGACACATAAGCAGGCTTGTACACAACCAGATCATTTGGAC
CATATAATTCCAGACCACGACTTCCTTTTTCCAGAATTTGCAGTTGTAGTAGAAACAGAAGATGAAGATTACACCTGAGG
TTGTGGAAAAGCAAGATTACTCAGAGATTATAGGGAACATGGGTGACGCACTTGAAGAAGAACTGGATTCCATGGCAAAA
CATGAATCCAGGGAAGATAAAATTTTTCAGAAGTTCAAAACTCAGATAGCCCTTGAACCAGAACAGATTCTCAGATATGG
CAGAGGTATTGCCCCCATCTGGATTCTAGTGAAAATATTCCTCAAGAAAAGGATATTCCAGAGAATATCCTTTGTGATGC
CAAGAAAATGTTTGAATTCCAGGTTATGCCTCAGCTCCTAAACTACCTGAAGGCTGACAGACTGGGCAAGAACATTGACT
GGGGCATCCTGGCTGTCTTCACCTGGGCTGAGAGCTGCATCTTGAGTACTGGCTATACAGAATAATTTGTGTGGAAGCAG
GATGTAACAGATACA

Alignment

ORF - retro_ggor_2876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.39 %
• Parental protein coverage: 86.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RALACELCGRPLSFLLQVYAPLPGRPDAFHRCIFLFCCREQPCCAGLRVFRNQLPRKNDFYSYEPPSENP
          ..LAC.LC...LSFLLQVYA.LPGR..AFH..IFLFCC.E.PCCAGLRVF.NQLPRKNDF.SY.PPSENP
Retrocopy QTLACALCCCQLSFLLQVYALLPGRAAAFHPGIFLFCC*EPPCCAGLRVFTNQLPRKNDFSSYGPPSENP

Parental  PPETGESVCLQLKSGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQ-TLDWRLGHKQACAQPDHLDHIIPDH
          .PETG.SVCL.LKSGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQ.TLD.RL.HKQAC.QPDHLDHIIPDH
Retrocopy LPETGQSVCL*LKSGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQ>TLDRRLTHKQACTQPDHLDHIIPDH

Parental  NFLFPEFEIVIETEDE-IMPEVVEKEDYSEIIGSMGEALEEELDSMAKHESREDKIFQKFKTQIALEPEQ
          .FLFPEF..V.ETEDE.I.PEVVEK.DYSEIIG.MG.ALEEELDSMAKHESREDKIFQKFKTQIALEPEQ
Retrocopy DFLFPEFAVVVETEDE>ITPEVVEKQDYSEIIGNMGDALEEELDSMAKHESREDKIFQKFKTQIALEPEQ

Parental  ILRYGRGIAPIWI-SGENIPQEKDIPD-CPCGAKRILEFQVMPQLLNYLKADRLGKSIDWGILAVFTCAE
          ILRYGRGIAPIWI.S.ENIPQEKDIP....C.AK...EFQVMPQLLNYLKADRLGK.IDWGILAVFT.AE
Retrocopy ILRYGRGIAPIWI<SSENIPQEKDIPENILCDAKKMFEFQVMPQLLNYLKADRLGKNIDWGILAVFTWAE

Parental  SCSLGTGYTEEFVWKQDVTDT
          SC.L.TGYTE.FVWKQDVTDT
Retrocopy SCILSTGYTE*FVWKQDVTDT

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	0.04 RPM	16.44 RPM
SRP007412_liver	0.00 RPM	11.98 RPM
SRP007412_testis	0.00 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_2876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2876 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4305
Pongo abelii	retro_pabe_3505

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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,