RetrogeneDB ID: retro_pabe_1738

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1_random:720242..721204(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSPPYG00000004356
• Aliases: None
• Description: lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]

Sequence

>retro_pabe_1738
ATGGCAACTCTTAAGGAAAAACTCATTGCACCAGTTGTAGAAGAGGCAACAGTCCCAGACAATAAGATCACTGTACTGGG
TGTTGGACAAATGGGTGTGGTGTGTGCTATCAGCATCTGGAAAAGTCTTTGGTTGATGAACTTCTTCTTGTGGATGTTTT
GGAACACGAGCTTAAAGGAGAAATGATGGATCAATCTGCAGATAGGAGTATATTTCCTCAGACACCTAAAATTGTGGCAG
ATAAAGATTATTCTATGACTGCCAATTAAAAGATTGTAGCGGTAACTGCAGGAGTCCATCAGCAAGAGGGGGAGAGTCGT
CTCAATCTGGTACAGAGAAATGTTAATGCCTTCAAATCTGTTGTTTCTCAGATCATTAAGTACAGTTCTAATTACATCAT
AATTGTGATTTCCAACCCATTGGCCGTTCTTACCTATGTTACCTGGAAACTAAGTGGATTACCCAAGCACCTTGTGATTG
GAAGTGGGTATAATTTGGATTCTGCTAGATTTTGCCACCTTGTGGCTGAAAAACTTGGCATTCATCTCGGCAGCTGCCAT
GGATGGATTTTGGGAGAACATGGTAATTCAAGTGTTGTTGTTCAGAGTGGTGTGAACATGGCAGGTGCTTCTCTCCAGGA
ATTGAATCCAGAAATGGGAACCAACAATGATCGTGAAACTTGGAAGGAAGTGCGTAAGATGGTGGTTGAAAGTGCCTATG
AGGTCAACAAGCCAAAAGGATATACCAACTGGGCTACTAGATTAAGTGTAGCTGATCTTGTTGAATCCATGTTGAAAAAT
CTATCCAGGATTCATCCAGAATGAACAATGATGAAGGGGATGAAGGGCATTGAGAATGAAGTCTTCCAGAGCCTTCCATG
TATCCTCAATACTCGGGAATTAACCAGCATTATCAACCAGAAGCTAAAGGATGATGAGTTTGCTCAGCTCAAGAAAAGTG
CA

Alignment

ORF - retro_pabe_1738 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.26 %
• Parental protein coverage: 96.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATLKEKLIAPVAEEEATVPNNKITVVGVGQVGMACAISI-LGKSLADELALVDVLEDKLKGEMMDLQHG
          MATLKEKLIAPV.EE.ATVP.NKITV.GVGQ.G..CAISI.L.KSL.DEL.LVDVLE..LKGEMMD....
Retrocopy MATLKEKLIAPVVEE-ATVPDNKITVLGVGQMGVVCAISI<LEKSLVDELLLVDVLEHELKGEMMDQSAD

Parental  -SLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVS
          .S.F.QTPKIVADKDYS.TAN.KIV.VTAGV.QQEGESRLNLVQRNVN.FK....QI.KYS...IIIV.S
Retrocopy RSIFPQTPKIVADKDYSMTAN*KIVAVTAGVHQQEGESRLNLVQRNVNAFKSVVSQIIKYSSNYIIIVIS

Parental  NPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVA
          NP...LTYVTWKLSGLPKH.VIGSG.NLDSARF..L.AEKLGIH..SCHGWILGEHG.SSV.V.SGVN.A
Retrocopy NPLAVLTYVTWKLSGLPKHLVIGSGYNLDSARFCHLVAEKLGIHLGSCHGWILGEHGNSSVVVQSGVNMA

Parental  GVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMV
          G.SLQELNPEMGT.ND.E.WKEV.KMVVESAYEV.K.KGYTNWA..LSVADL.ESMLKNLSRIHP..TM.
Retrocopy GASLQELNPEMGTNNDRETWKEVRKMVVESAYEVNKPKGYTNWATRLSVADLVESMLKNLSRIHPE*TMM

Parental  KGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSA
          KGM.GIENEVF.SLPCILN.R.LTS.INQKLKDDE.AQLKKSA
Retrocopy KGMKGIENEVFQSLPCILNTRELTSIINQKLKDDEFAQLKKSA

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	504.36 RPM
SRP007412_cerebellum	0.00 RPM	372.22 RPM
SRP007412_heart	0.03 RPM	1192.91 RPM
SRP007412_kidney	0.03 RPM	860.49 RPM
SRP007412_liver	0.00 RPM	33.91 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1738 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1738 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1738 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016175	4 retrocopies	retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Canis familiaris	ENSCAFG00000012195	9 retrocopies	retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Echinops telfairi	ENSETEG00000019955	1 retrocopy	retro_etel_850,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Macropus eugenii	ENSMEUG00000004825	1 retrocopy	retro_meug_311,
Myotis lucifugus	ENSMLUG00000012155	1 retrocopy	retro_mluc_202,
Macaca mulatta	ENSMMUG00000002679	4 retrocopies	retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica	ENSMODG00000017786	1 retrocopy	retro_mdom_1484,
Mustela putorius furo	ENSMPUG00000000172	5 retrocopies	retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Pongo abelii	ENSPPYG00000003435	2 retrocopies	retro_pabe_203, retro_pabe_779,
Pongo abelii	ENSPPYG00000003437	5 retrocopies	retro_pabe_2002, retro_pabe_2039, retro_pabe_2423, retro_pabe_3407, retro_pabe_364,
Pongo abelii	ENSPPYG00000004356	3 retrocopies	retro_pabe_1738 , retro_pabe_1744, retro_pabe_3780,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,
Tarsius syrichta	ENSTSYG00000013759	7 retrocopies	retro_tsyr_1130, retro_tsyr_1532, retro_tsyr_1860, retro_tsyr_2051, retro_tsyr_334, retro_tsyr_64, retro_tsyr_986,