RetrogeneDB ID: retro_pabe_2624

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:29986400..29987011(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLG2
• Ensembl ID: ENSPPYG00000013735
• Aliases: None
• Description: succinate-CoA ligase, GDP-forming, beta subunit [Source:HGNC Symbol;Acc:11450]

Sequence

>retro_pabe_2624
CTGGTAGCGCAAGCCAGGAAACTTCTGAGAGACCTAGCGCTCCACTGTGGTTCTTGGTAGCCAGGTCCAGGCACTTCAAT
TAACTTCCAGAAGATGGCAGACCCTCCAGGAATGCCAGAGCAAGAAACTGATGTCTGACAACAGAGTGAGAGTTCAAAGA
TTCTTTGTAGCAGACACTGTGAATGAAGAACTTGAGGTTGCTAAGAGACTAAAAGCAAAATAAATTGTTTTAATTAAAAG
CCTAGATCTTAGCTGGAGGAAGAGGAAAGGGTGTCTTCAATTGTGGTTCGAAAGGAGGTGTTCTCTTAACAAAAGAACCT
AAAGTTGTGGGACAGCTGGCTAAACAGATGATTGGGTATGTTTGGGGCAATAAACCAAACTCTAAAAGAAGATGTGAAAG
TTAACAAGCTGATGGTTACTGAAACCTTGGTCATTTCCAGAAAAACTTACCTGGTGATTCTAATGGACAGGTCCTGCAAT
AGCCCCATGCTGGTGGGCAGGCCCCAGGGGGCACTGACATTGAAGAGGTGGCTGCTACAAATTCAGAATTTATTTTTAAG
GAGCAAATTTTTCAAGGGATAAAGGACAGCCAAGTTCAGAGTTCAGCAGAT

Alignment

ORF - retro_pabe_2624 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.19 %
• Parental protein coverage: 51.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VAAQAGKLLRALVLRPR-FLAAGS-QAVQLTSRRWLNLQEYQSKKLMSDNGVRVQRFFVADTANEALEAA
          ..AQA.KLLR.L.L....FL.A.S.QA.QLTSRRW..LQE.QSKKLMSDN.VRVQRFFVADT.NE.LE.A
Retrocopy LVAQARKLLRDLALHCG<FLVARS<QALQLTSRRWQTLQECQSKKLMSDNRVRVQRFFVADTVNEELEVA

Parental  KRLNAKEIVL-KAQILAGGRGKG-VFNSGLKGGVHLTKDPNVVGQLAKQMIGYNLATK-QTPKEGVKVNK
          KRL.AK.IVL.K...L.....KG.VFN.G.KGGV.LTK.P.VVGQLAKQMIGY....K.QT.KE.VKVNK
Retrocopy KRLKAK*IVLIKSLDLSWRKRKG>VFNCGSKGGVLLTKEPKVVGQLAKQMIGYVWGNK>QTLKEDVKVNK

Parental  VMVAEALDISRETYLAILMDRSCNGPVLVGSPQ-GGVDIEEVAASNPELIFKEQIDIFEGIKDSQAQRMA
          .MV.E.L.ISR.TYL.ILMDRSCN.P.LVG.PQ.GG.DIEEVAA.N.E.IFKEQ..IF.GIKDSQ.Q..A
Retrocopy LMVTETLVISRKTYLVILMDRSCNSPMLVGRPQ<GGTDIEEVAATNSEFIFKEQ--IFQGIKDSQVQSSA

Parental  E
          .
Retrocopy D

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	9.29 RPM
SRP007412_cerebellum	0.00 RPM	4.50 RPM
SRP007412_heart	0.00 RPM	75.44 RPM
SRP007412_kidney	0.00 RPM	84.69 RPM
SRP007412_liver	0.00 RPM	62.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2624 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2624 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2624 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1995

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000172340	1 retrocopy	retro_hsap_1044,
Gorilla gorilla	ENSGGOG00000027438	1 retrocopy	retro_ggor_825,
Myotis lucifugus	ENSMLUG00000017294	1 retrocopy	retro_mluc_695,
Macaca mulatta	ENSMMUG00000009693	2 retrocopies	retro_mmul_1273, retro_mmul_1995,
Mus musculus	ENSMUSG00000061838	1 retrocopy	retro_mmus_3720,
Nomascus leucogenys	ENSNLEG00000007553	1 retrocopy	retro_nleu_915,
Otolemur garnettii	ENSOGAG00000006190	1 retrocopy	retro_ogar_161,
Pongo abelii	ENSPPYG00000005352	2 retrocopies	retro_pabe_1939, retro_pabe_2852,
Pongo abelii	ENSPPYG00000013735	1 retrocopy	retro_pabe_2624 ,
Pteropus vampyrus	ENSPVAG00000004554	1 retrocopy	retro_pvam_912,