RetrogeneDB ID: retro_pabe_93

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:57501360..57502107(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000025829
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000005333
• Aliases: None
• Description: None

Sequence

>retro_pabe_93
ATGGCCGAGCGCGGGGAACTCGACTTGACCGGCGCCAAACAGAACACAGGAGTGTGGCTAGTCAAGGTTCCTAAATATTT
GTCAAAGCAATGGGGTAAAGCCTCTGGAAGAGGTGAAGTTGGGAAACTGCGGATTGCCAAGACTCAGGGAAGGACTGAGG
TGTCATTTACTTTGAATGAGGATCTTGCAAATATTCATGATATTGGTGGAAAACCAGCTTCAGTCAGTGCTCCTAGAGAA
CATCCATTTGTCTTGCAAAGTGTTGGAGGACAGACATTAACAGTATTTACTGAGAGCTCATCAGATAAGCTGTCATTGGA
AGGAATAGTGGTACAAAGAGCTGAGTGCCGACCAGCTGCCAGTGAAAACTACATGCGATTAAAAAGATTGCAAATAGAAG
AGTCTTCCAAACCTGTGAGGCTATCACAACAGCTGGACAAAGTTGTAACAACCAATTACAAACCTGTTGCTAATCATCAA
TACAATATTGAATATGAAAGGAAAAAGAAAGGAGACGGGAAGCGAGCTCGAGCTGATAAACAACATGTTTTAGACATGCT
ATTTTCAGCCTTTGAGAAACATCAATACTATAATCTTAAGGACTTGGTGGACATCACAAAACAACCTGTGGTGTACCTGA
AGGAAATCTTAAGAGAAATTGGTGTTCAGAATGTAAAAGGGATCCACAAAAACACATGGGAGCTGAAGCCAGAGTACAGA
CACTATCAAGGAGAAGAAAAGAGTGAC

Alignment

ORF - retro_pabe_93 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAERGELDLTGAKQNTGVWLVKVPKYLSQQWAKASGRGEVGKLRIAKTQGRTEVSFTLNEDLANIHDIGG
          MAERGELDLTGAKQNTGVWLVKVPKYLS.QW.KASGRGEVGKLRIAKTQGRTEVSFTLNEDLANIHDIGG
Retrocopy MAERGELDLTGAKQNTGVWLVKVPKYLSKQWGKASGRGEVGKLRIAKTQGRTEVSFTLNEDLANIHDIGG

Parental  KPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPAASENYMRLKRLQIEESSKPVR
          KPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPAASENYMRLKRLQIEESSKPVR
Retrocopy KPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPAASENYMRLKRLQIEESSKPVR

Parental  LSQQLDKVVTTNYKPVANHQYNIEYERKKKEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPV
          LSQQLDKVVTTNYKPVANHQYNIEYERKKK.DGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPV
Retrocopy LSQQLDKVVTTNYKPVANHQYNIEYERKKKGDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPV

Parental  VYLKEILKEIGVQNVKGIHKNTWELKPEYRHYQGEEKSD
          VYLKEIL.EIGVQNVKGIHKNTWELKPEYRHYQGEEKSD
Retrocopy VYLKEILREIGVQNVKGIHKNTWELKPEYRHYQGEEKSD

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	5.42 RPM
SRP007412_cerebellum	0.00 RPM	4.26 RPM
SRP007412_heart	0.03 RPM	4.12 RPM
SRP007412_kidney	0.00 RPM	5.20 RPM
SRP007412_liver	0.09 RPM	5.72 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_93 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_93 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_93 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028333	1 retrocopy	retro_acar_174,
Bos taurus	ENSBTAG00000034495	2 retrocopies	retro_btau_1753, retro_btau_208,
Choloepus hoffmanni	ENSCHOG00000007391	1 retrocopy	retro_chof_1718,
Callithrix jacchus	ENSCJAG00000019220	2 retrocopies	retro_cjac_1351, retro_cjac_2990,
Felis catus	ENSFCAG00000002105	1 retrocopy	retro_fcat_526,
Homo sapiens	ENSG00000188342	2 retrocopies	retro_hsap_2990, retro_hsap_368,
Gorilla gorilla	ENSGGOG00000006657	2 retrocopies	retro_ggor_2070, retro_ggor_379,
Myotis lucifugus	ENSMLUG00000010505	1 retrocopy	retro_mluc_58,
Macaca mulatta	ENSMMUG00000012634	2 retrocopies	retro_mmul_1913, retro_mmul_483,
Monodelphis domestica	ENSMODG00000025484	1 retrocopy	retro_mdom_231,
Nomascus leucogenys	ENSNLEG00000002097	1 retrocopy	retro_nleu_2440,
Nomascus leucogenys	ENSNLEG00000002106	1 retrocopy	retro_nleu_742,
Otolemur garnettii	ENSOGAG00000012517	1 retrocopy	retro_ogar_2772,
Procavia capensis	ENSPCAG00000005868	3 retrocopies	retro_pcap_102, retro_pcap_173, retro_pcap_375,
Pongo abelii	ENSPPYG00000005333	1 retrocopy	retro_pabe_93 ,
Pan troglodytes	ENSPTRG00000005840	3 retrocopies	retro_ptro_2022, retro_ptro_288, retro_ptro_2932,
Pteropus vampyrus	ENSPVAG00000014092	1 retrocopy	retro_pvam_1490,
Rattus norvegicus	ENSRNOG00000029316	1 retrocopy	retro_rnor_1288,
Ictidomys tridecemlineatus	ENSSTOG00000006891	1 retrocopy	retro_itri_19,
Tursiops truncatus	ENSTTRG00000002729	2 retrocopies	retro_ttru_1003, retro_ttru_850,