RetrogeneDB ID: retro_pabe_958

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:109697911..109698442(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000017193
• Aliases: None
• Description: None

Sequence

>retro_pabe_958
CTGGCCTGCGCGCTGTGCGGCCGTAGCTCTTCTTCCCGCGGCAGGGGTACGCGTCGCTGCCCGGCCGCGCCGACGCCTTC
CACCGTGGCATCTTCCTCTTCTGCTGCCACGAGTCGCCGTACTGTGCCGCCCTGCGAGTTGCTAGGAATCAGCTACCCAG
GAAAAATGATTTTTACTCATATGAGCCACCTTCTGAGAATCCTCCCCTAGAAACAGGAGAATCCGTGTATCTCCAACTTA
TGTCTGGTGCTCATATCTGCAGGGTTTGTGGCTGTTTAGGCCCCCAAAATTTGCTCCAGATGCCACAAAGCGTATTACTG
CAGCAAGGAGCATCAGACCCTAGACTGGAGATTGGGACATAAGCAGGCTTATGCACAACCAGATCATTTGGACCTTACAA
CTCCAGACCACGACTTCCTTTTTCCAGAATTTGAAATTGTAATAGAAACAGAAGATGAGATTATGCCTGAGGTTGCGGAA
AAGGAAGATTATTCAGAGATTATAGGGAGCATGGTTAAGCAGTTTCAGGAC

Alignment

ORF - retro_pabe_958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.01 %
• Parental protein coverage: 51.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LACELCGRPLS-FLLQVYAPLPGRPDAFHRCIFLFCCREQPCCAGLRVFRNQLPRKNDFYSYEPPSENPP
          LAC.LCGR..S.F..Q.YA.LPGR.DAFHR.IFLFCC.E.P.CA.LRV.RNQLPRKNDFYSYEPPSENPP
Retrocopy LACALCGRSSS<FPRQGYASLPGRADAFHRGIFLFCCHESPYCAALRVARNQLPRKNDFYSYEPPSENPP

Parental  PETGESVCLQLKSGAHLCRVCGCLGP-KTCSRCHKAYYCSKEHQTLDWRLGHKQACAQPDHLDHIIPDHN
          .ETGESV.LQL.SGAH.CRVCGCLGP.K.CSRCHKAYYCSKEHQTLDWRLGHKQA.AQPDHLD...PDH.
Retrocopy LETGESVYLQLMSGAHICRVCGCLGP>KICSRCHKAYYCSKEHQTLDWRLGHKQAYAQPDHLDLTTPDHD

Parental  FLFPEFEIVIETEDEIMPEVVEKEDYSEIIESMGEALEE
          FLFPEFEIVIETEDEIMPEV.EKEDYSEII.SM......
Retrocopy FLFPEFEIVIETEDEIMPEVAEKEDYSEIIGSMVKQFQD

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	6.97 RPM
SRP007412_cerebellum	0.00 RPM	11.55 RPM
SRP007412_heart	0.00 RPM	7.22 RPM
SRP007412_kidney	0.03 RPM	14.65 RPM
SRP007412_liver	0.00 RPM	13.37 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_958 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_958 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_958 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_788
Gorilla gorilla	retro_ggor_899

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 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,
Cavia porcellus	ENSCPOG00000002920	1 retrocopy	retro_cpor_168,
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,
Ictidomys tridecemlineatus	ENSSTOG00000022768	2 retrocopies	retro_itri_1348, retro_itri_1635,