RetrogeneDB ID: retro_pabe_2478

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:156400166..156400664(+)
• Located in intron of: ENSPPYG00000015116

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000001589
• Aliases: None
• Description: None

Sequence

>retro_pabe_2478
GCAGTAATGGCACAGAAAGAGGGAGATGTTAGAGATTACAATTTGACTGAGGAACAGAAGGCGATCAAGGCCAACTATCC
GCCAGTCAATAGGAATTACGAGTATTTGGATCATACAGCAGATGTCCAGTTACACACATGGGGAGATACTCTGGAGGAAG
CATTTGAGCAATGTGCAATGGCCATATTTGGTTACATGATAGATACCAGGACTGTGGAGCCTCTCCAAACAATAGAAGTA
GAAACCCAAGATGTTTCTACTTTTCTTTTTCACTTTTTAGATGAGTGGCTTCATAAGTCCAATGCTGATGAATTCTTCAT
ACCCTGGGAAGTGAAAGTACTTTGTATTGATCAAAGACATTTCCAATTACAATCAGTTGGGTGGAGAGAATGTTTATTGT
CCAAGCACCCTCAGGGAACAGAAGTCAAAGTTATAACATATTCAGCAATGCAGGTCTATAATTAAGAAAACCCAGAAGTT
TTTGTGATCATTGACATT

Alignment

ORF - retro_pabe_2478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.66 %
• Parental protein coverage: 94.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVMAQEEEDVRDYNLTEEQKAIKAKYPPVNRKYEYLDHTADVQLHAWGDTLEEAFEQCAMAMFGYMTDTG
          AVMAQ.E.DVRDYNLTEEQKAIKA.YPPVNR.YEYLDHTADVQLH.WGDTLEEAFEQCAMA.FGYM.DT.
Retrocopy AVMAQKEGDVRDYNLTEEQKAIKANYPPVNRNYEYLDHTADVQLHTWGDTLEEAFEQCAMAIFGYMIDTR

Parental  TVEPLQTVEVETQGDDLQSLLFHFLDEWLYKFSADEFFIPREVKVLSIDQRNFKLRSIGWGEEFSLSKHP
          TVEPLQT.EVETQ..D....LFHFLDEWL.K..ADEFFIP.EVKVL.IDQR.F.L.S.GW..E..LSKHP
Retrocopy TVEPLQTIEVETQ--DVSTFLFHFLDEWLHKSNADEFFIPWEVKVLCIDQRHFQLQSVGW-RECLLSKHP

Parental  QGTEVKAITYSAMQVYNEEKPEVFVIIDI
          QGTEVK.ITYSAMQVYN.E.PEVFVIIDI
Retrocopy QGTEVKVITYSAMQVYN*ENPEVFVIIDI

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	0.06 RPM	13.38 RPM
SRP007412_cerebellum	0.00 RPM	15.56 RPM
SRP007412_heart	0.00 RPM	11.83 RPM
SRP007412_kidney	0.03 RPM	28.11 RPM
SRP007412_liver	0.00 RPM	18.61 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2478 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2478 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2478 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2992
Gorilla gorilla	retro_ggor_2072
Macaca mulatta	retro_mmul_1915

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010550	1 retrocopy	retro_cfam_2152,
Choloepus hoffmanni	ENSCHOG00000004061	2 retrocopies	retro_chof_1005, retro_chof_1158,
Cavia porcellus	ENSCPOG00000015349	2 retrocopies	retro_cpor_356, retro_cpor_903,
Dasypus novemcinctus	ENSDNOG00000001861	2 retrocopies	retro_dnov_1056, retro_dnov_2193,
Equus caballus	ENSECAG00000020982	1 retrocopy	retro_ecab_610,
Felis catus	ENSFCAG00000000700	1 retrocopy	retro_fcat_703,
Homo sapiens	ENSG00000176261	2 retrocopies	retro_hsap_2396, retro_hsap_2992,
Gorilla gorilla	ENSGGOG00000007519	2 retrocopies	retro_ggor_2072, retro_ggor_231,
Myotis lucifugus	ENSMLUG00000000745	5 retrocopies	retro_mluc_1961, retro_mluc_2533, retro_mluc_2570, retro_mluc_2617, retro_mluc_2622,
Macaca mulatta	ENSMMUG00000009939	1 retrocopy	retro_mmul_1915,
Monodelphis domestica	ENSMODG00000017419	2 retrocopies	retro_mdom_400, retro_mdom_901,
Mus musculus	ENSMUSG00000057572	1 retrocopy	retro_mmus_2631,
Oryctolagus cuniculus	ENSOCUG00000000940	1 retrocopy	retro_ocun_492,
Otolemur garnettii	ENSOGAG00000011630	1 retrocopy	retro_ogar_3231,
Pongo abelii	ENSPPYG00000001589	2 retrocopies	retro_pabe_13, retro_pabe_2478 ,
Tursiops truncatus	ENSTTRG00000014968	1 retrocopy	retro_ttru_1200,