RetrogeneDB ID: retro_pabe_241

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:51706152..51706645(+)
• Located in intron of: ENSPPYG00000000380

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEBP1
• Ensembl ID: ENSPPYG00000005011
• Aliases: None
• Description: Phosphatidylethanolamine-binding protein 1 Hippocampal cholinergic neurostimulating peptide [Source:UniProtKB/Swiss-Prot;Acc:Q5R4R0]

Sequence

>retro_pabe_241
TTCCCTGGCTAGTTTTCAGAGGCTGCCAAGTCGCCGCTGCGCCCGCGCCTTGCCTAGTGGCACTCCCAGCTGCGCGCTCC
GTTCTTGCGCAGCCATGCCAAGGACCTCAGCAAGCGGTCCAGGCCCTTGAGCCTGCAGGAAGTGGACGGGCAGCCGCAGC
ACTCGCTGCATGTCACCTACGCCAGGGCGGCGGTGGACGAGCTGGGCAAAGTGCTGACACCCACCTAGGTTAACAGACCC
ACCAGCATTTCATGGGATGATCTTGATTCAAGGAAACTCTACACCTTGGTCCTAACAGACCCGGATGCTCCCGGCAGGAA
GAAGCCCCAGTACAGTGAATGGCGTCATTTCCTGGTGGTCAACATGAAGGGTAATGACGTTAGCAGTGGCCCAGTCTTCT
CCATTACGTGGGCTCGGGCCTCCAGAGGGCACAGGTCTCCACCGCTATGTCTGGCTGGTTTACAAACAGGACTGGCTGCT
GAAGTGTGACGAG

Alignment

ORF - retro_pabe_241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.0 %
• Parental protein coverage: 62.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FPGQCAELSVSSLPPAPGLP-RHSRLHPLLGFAMPVDLSKWSGPLSLQEVDERPQHPLHVTYAGAAVDEL
          FPG...E...S..P..P.L...HS.L..........DLSK.S.PLSLQEVD..PQH.LHVTYA.AAVDEL
Retrocopy FPG*FSEAAKS--PLRPRLA*WHSQLRAPFLRSHAKDLSKRSRPLSLQEVDGQPQHSLHVTYARAAVDEL

Parental  GKVLTPTQVKNRPTSISWEGLDSGKLYTLVLTDPDAPSRKDPKYREWHHFLVVNMKGNDISSGTVLS-DY
          GKVLTPT.V.NRPTSISW..LDS.KLYTLVLTDPDAP.RK.P.Y.EW.HFLVVNMKGND.SSG.V.S..Y
Retrocopy GKVLTPT*V-NRPTSISWDDLDSRKLYTLVLTDPDAPGRKKPQYSEWRHFLVVNMKGNDVSSGPVFS<HY

Parental  VGS-GPPKGTGLHRYVWLVYEQDRPLKCDE
          VGS.GPP.GTGLHRYVWLVY.QD..LKCDE
Retrocopy VGS<GPPEGTGLHRYVWLVYKQDWLLKCDE

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	583.10 RPM
SRP007412_cerebellum	0.00 RPM	564.47 RPM
SRP007412_heart	0.00 RPM	255.07 RPM
SRP007412_kidney	0.07 RPM	522.13 RPM
SRP007412_liver	0.09 RPM	418.63 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_241 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_241 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_241 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016143	2 retrocopies	retro_amel_1355, retro_amel_754,
Bos taurus	ENSBTAG00000018115	2 retrocopies	retro_btau_1183, retro_btau_705,
Canis familiaris	ENSCAFG00000009910	1 retrocopy	retro_cfam_526,
Callithrix jacchus	ENSCJAG00000009314	2 retrocopies	retro_cjac_1410, retro_cjac_818,
Erinaceus europaeus	ENSEEUG00000003689	1 retrocopy	retro_eeur_292,
Felis catus	ENSFCAG00000002277	3 retrocopies	retro_fcat_1317, retro_fcat_1360, retro_fcat_299,
Homo sapiens	ENSG00000089220	3 retrocopies	retro_hsap_1456, retro_hsap_2288, retro_hsap_492,
Gorilla gorilla	ENSGGOG00000013281	3 retrocopies	retro_ggor_1121, retro_ggor_1701, retro_ggor_461,
Myotis lucifugus	ENSMLUG00000002259	7 retrocopies	retro_mluc_103, retro_mluc_1612, retro_mluc_1742, retro_mluc_2357, retro_mluc_2373, retro_mluc_984, retro_mluc_998,
Macaca mulatta	ENSMMUG00000005098	4 retrocopies	retro_mmul_1621, retro_mmul_2272, retro_mmul_328, retro_mmul_442,
Mustela putorius furo	ENSMPUG00000002861	3 retrocopies	retro_mputfur_1228, retro_mputfur_1361, retro_mputfur_223,
Mus musculus	ENSMUSG00000032959	4 retrocopies	retro_mmus_138, retro_mmus_1857, retro_mmus_2314, retro_mmus_542,
Oryctolagus cuniculus	ENSOCUG00000008395	2 retrocopies	retro_ocun_1329, retro_ocun_1900,
Otolemur garnettii	ENSOGAG00000001740	1 retrocopy	retro_ogar_2750,
Pongo abelii	ENSPPYG00000005011	2 retrocopies	retro_pabe_1202, retro_pabe_241 ,
Pan troglodytes	ENSPTRG00000005512	3 retrocopies	retro_ptro_1621, retro_ptro_371, retro_ptro_992,
Rattus norvegicus	ENSRNOG00000001136	3 retrocopies	retro_rnor_1223, retro_rnor_46, retro_rnor_541,
Ictidomys tridecemlineatus	ENSSTOG00000004085	2 retrocopies	retro_itri_1603, retro_itri_961,
Tupaia belangeri	ENSTBEG00000000177	2 retrocopies	retro_tbel_272, retro_tbel_2728,
Tursiops truncatus	ENSTTRG00000000658	1 retrocopy	retro_ttru_1164,