RetrogeneDB ID: retro_ptro_788

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:108267505..108268013(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD2
• Ensembl ID: ENSPTRG00000018828
• Aliases: None
• Description: programmed cell death 2 [Source:HGNC Symbol;Acc:8762]

Sequence

>retro_ptro_788
TTGGCCTCAGAGCTGTGCGACCGTCGCTCTTCTTCCGGCGGCAGGTGTACGCGTCGTTGCCCGGCCGCGCAGACGCCTTC
CACCGCATCTTCCTCTTCTGCTGCCACGAGCCGCCGTGCTGTGCCGCCCTGCGAGTTTCTAGGAATCAGCTACCCAGGAA
AAATGATTTTTACTCATATGAGCCACCTTCTGAGAATCCTTCCCCAGAAACAGGAGAATCGGTGTATCTCCAACTTAAGT
CTGGTGCTCATCTCTGCAGGGTTTGTGGCTATTTAGGCCCCAAAACTTGCTCCAGATGCCACAAAGCGTATTACTGCGCA
AGGAGCATCAGACCCTAGACTGGAGATTGGGACATAAGCAGGCTTGTGCACAACCAGATCATTTGGACCTTACAACTCCA
GACCACAACTTCGTTTTTCCAGAATTTGAAATTGTAATAGAAACAGAAGATGAGATTATGCCTGAGGTTGCGGAAAAGGA
AGATTATTCAGATATTATAGGGAGCATG

Alignment

ORF - retro_ptro_788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.55 %
• Parental protein coverage: 50.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LACELCGR-PLSFLLQVYAPLPGRPDAFHRCIFLFCCREQPCCAGLRVFRNQLPRKNDFYSYEPPSENPP
          LA.ELC.R..L.F..QVYA.LPGR.DAFHR.IFLFCC.E.PCCA.LRV.RNQLPRKNDFYSYEPPSENP.
Retrocopy LASELCDR<SLFFRRQVYASLPGRADAFHR-IFLFCCHEPPCCAALRVSRNQLPRKNDFYSYEPPSENPS

Parental  PETGESVCLQLKSGAHLCRVCGCLGPKTCSRCHKAYYCS-KEHQTLDWRLGHKQACAQPDHLDHIIPDHN
          PETGESV.LQLKSGAHLCRVCG.LGPKTCSRCHKAYYC..KEHQTLDWRLGHKQACAQPDHLD...PDHN
Retrocopy PETGESVYLQLKSGAHLCRVCGYLGPKTCSRCHKAYYCA<KEHQTLDWRLGHKQACAQPDHLDLTTPDHN

Parental  FLFPEFEIVIETEDEIMPEVVEKEDYSEIIGSM
          F.FPEFEIVIETEDEIMPEV.EKEDYS.IIGSM
Retrocopy FVFPEFEIVIETEDEIMPEVAEKEDYSDIIGSM

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	0.54 RPM	7.29 RPM
SRP007412_cerebellum	0.07 RPM	6.35 RPM
SRP007412_heart	0.26 RPM	5.10 RPM
SRP007412_kidney	0.26 RPM	10.46 RPM
SRP007412_liver	0.00 RPM	4.68 RPM
SRP007412_testis	0.63 RPM	11.70 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_788 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_788 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_788 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_899
Pongo abelii	retro_pabe_958

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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,