RetrogeneDB ID: retro_pabe_151

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:547937..548774(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000016163
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000025821
• Aliases: None
• Description: None

Sequence

>retro_pabe_151
ATGAAGTTTCGCGCCAAGATCACCGGCCAAGGCTGTCTAGAGCTGTTCATCCACGTCAGCGGCACCGTCGCGAGGCTGGC
GAAGGTGTGCGTGCTCCGCGTGTGCCCTGACAGCCTGTGCTTCGGCCCCGCGGGCTCCGGCGGCCTCCGCGAGGCCAGGC
TGTGGTGCGAGGTGCGGCAGGGGGCCTTCCAGCAGTTTCGCATGGAAGGTGTCTCGGAAGACCTCAATGAGATCCACCTG
GAGCTGACGGCGGAGCACCTGTCCCGGGCGGCGAGAAGCGCAGCGGGCGCGTCCTCCCTGAAGCTGCAGCTGACCCACAA
GCGGCGCCCCTGCCTCACGGTGGCGGTGGAGCTGGTCTCGTCCCTGGGCCGCTCTCGCAGCGTGTTGCACGATCTGCCCG
TGCGGGTGCTTCCCAGAAGAGTGTGGCGGGACTGCCTGCCGCCCAGCCTGCGCGCCTCCGACGCGAGCATCTACCTGCCG
CGCTGGAGGACGCTGAGGAGCATCGTGGAGAGGATGGCGAACGTGGGCGATCACGTGCTGGTGGAAGCAAACCTCAGTGG
CAGGATGACCCTGAGTATAGAGACGGAGGTGGTGTCCATTCAAAGTTATTTTAAAAATCTTGGAAACCCTCCCAAGTCGG
CTGTGGGTGTGCCTCAAAACAGAGACCTGGAGAGCATGGTGCAAGTGCGGGTAGATAATCGGAAGCTTCTGCAGTGTTTG
GAGGGACAGCAAATACATCCTACGACGGCCCTGTGCAATATTTGGGACAATACTCTTCTTCAGCTTGTTTTGGTTCAAGA
AGATGTCTCTCTTCAGTATTTCATTCCTGCCTTGTAA

Alignment

ORF - retro_pabe_151 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFRAKIVDGACLNHFTRISNMIAKLAKTCTLRISPDKLNFILCDKLANGGVSMWCELEQENFFNEFQME
          MKFRAKI....CL..F...S...A.LAK.C.LR..PD.L.F.............WCE..Q...F..F.ME
Retrocopy MKFRAKITGQGCLELFIHVSGTVARLAKVCVLRVCPDSLCFGPAGSGGLREARLWCEVRQ-GAFQQFRME

Parental  GVSAENNEIYLELTSENLSRALKTAQNARALKIKLTNKHFPCLTVSVELLSMSSSSRIVTHDIPVKVIPR
          GVS...NEI.LELT.E.LSRA...A..A..LK..LT.K..PCLTV.VEL.S....SR.V.HD.PV.V.PR
Retrocopy GVSEDLNEIHLELTAEHLSRAARSAAGASSLKLQLTHKRRPCLTVAVELVSSLGRSRSVLHDLPVRVLPR

Parental  KLWKDLQEPVVPDPDVSIYLPVLKTMKSVVEKMKNISNHLVIEANLDGELNLKIETELVCVTTHFKDLGN
          ..W.D...P.....D.SIYLP...T..S.VE.M.N...H...EANL.G...L.IETE.V.....FK.LGN
Retrocopy RVWRDCLPPSLRASDASIYLPRWRTLRSIVERMANVGDHVLVEANLSGRMTLSIETEVVSIQSYFKNLGN

Parental  PPLASESTQKNRNVEHMAEVHIDIRKLLQFLAGQQVNPTKALCNIVSNKMVHFDLLHEDVSLQYFIPAL
          PP........NR..E.M..V..D.RKLLQ.L.GQQ..PT.ALCNI..N......L..EDVSLQYFIPAL
Retrocopy PPKSAVGVPQNRDLESMVQVRVDNRKLLQCLEGQQIHPTTALCNIWDNTLLQLVLVQEDVSLQYFIPAL

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	0.66 RPM
SRP007412_cerebellum	0.00 RPM	1.09 RPM
SRP007412_heart	0.00 RPM	1.14 RPM
SRP007412_kidney	0.07 RPM	1.76 RPM
SRP007412_liver	0.09 RPM	1.16 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_151 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_151 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_151 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001764	4 retrocopies	retro_chof_1438, retro_chof_1958, retro_chof_2084, retro_chof_898,
Dipodomys ordii	ENSDORG00000006582	1 retrocopy	retro_dord_182,
Echinops telfairi	ENSETEG00000009941	2 retrocopies	retro_etel_1764, retro_etel_1797,
Nomascus leucogenys	ENSNLEG00000004497	1 retrocopy	retro_nleu_2321,
Oryctolagus cuniculus	ENSOCUG00000027263	1 retrocopy	retro_ocun_761,
Otolemur garnettii	ENSOGAG00000012683	1 retrocopy	retro_ogar_1,
Pongo abelii	ENSPPYG00000025821	1 retrocopy	retro_pabe_151 ,
Sorex araneus	ENSSARG00000012348	1 retrocopy	retro_sara_391,
Ictidomys tridecemlineatus	ENSSTOG00000027204	1 retrocopy	retro_itri_151,