RetrogeneDB ID: retro_pabe_1905

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:31017837..31018978(-)
• Located in intron of: ENSPPYG00000011766

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA9
• Ensembl ID: ENSPPYG00000004171
• Aliases: None
• Description: NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001127602]

Sequence

>retro_pabe_1905
TTGTGGGAGATGGCGGCCGCTGCACAATCCCGGGTTGTCTGGGCCCTGCCAATGTCACATTCTGCCATTACTGCAATAGC
CACATCCGTGTGTCACAGTCCACTCCATTGCCAGCTTCATCATGCCCTCATACCTCATGGGAAAGGTGGATGTTCCTCAA
GTCAGTGGGATTGTGGCCACTGGGTTTGGAGCAACAGGATTCCTGGGATGATGTGTTGTCAACCACCTTGGACGCGTGGG
GTCACAGGTGATCATACCCTATCGGTGTGATACATGTGACATCATGCACCTTCGTCCCATGGGAGACCTGGGCTAGCTTC
TGTTTCTGGAATGGGACGCAAGAGATAAAGATTCTATCCAATGAGTAGTGGAACACAGCAATGTGGTCATAAATCTTGTT
GGACGAGACTGGGAAACCAAAAACTTTGATTTTGAGGATGTTTTTGTGAAGATTCCCCAAGCAATTGCTCAGGTGTCCAA
GGAAGCTGGAGTTGGAAAATTCATTCATGTTGCACATCTGAATGTGAATATTAAAAGCTCTTCTAGATATTTGAGAAATA
AGGCTGTTGGAGAGAAAGCAATGAGAGATGCATTTCCAGAAGCCATTATCGTAAAGCTGTTGGACATCTGTGGAAGAGAG
GATAGATTCCTTAATTATTTTGCAAATATGTGTTGGTTTGGCGCTATACCCCTTGTTTCCTTGGGCTGGAAGGCAGTTAA
ACAACCAGTATATGTTGTAGATGTATCCAAAGGAATTGTTAATGCAGTTAAGGAACCTGATGCCAACGGGAAAACCTTTG
CTTTCGTTGGGCCAAATCGGTACCTCCTCTTTGACCTGGTGAAGTACATCTTTGCTGTGGCTCACAGACTCTTCCTCCCA
TACCCCTTGCCACCTTTTGCCTATCAGTGGGTAGCAAGAGACTTTGAAATAAGCCTATTTGAGTCCTGGACAACAAGGAA
TAAAGTGGAGCGTATTCACATCACAGGCATGACCTTGTCTCACCTGCCAAGCTTAGAAGACCTTGGTATTCAGGCAACAC
CACTGGAACTCAAAGCCATTGAGGTGCTGTGGCTTCATCACACTTACTTCTGGCTGTCTGCTGAAATTGAGGATGTGAAG
CCGGCCAAGACTGTCAACATT

Alignment

ORF - retro_pabe_1905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LWEKMAAAAQSRVVRVLSMSRSAITAIATSVCHGPPRRQLHHALIPHGKGGRSS-VSGIVATVFGATGFL
          LWE.MAAAAQSRVV..L.MS.SAITAIATSVCH.P...QLHHALIPHGKGG.SS.VSGIVAT.FGATGFL
Retrocopy LWE-MAAAAQSRVVWALPMSHSAITAIATSVCHSPLHCQLHHALIPHGKGGCSS>VSGIVATGFGATGFL

Parental  GRYVVNHLGRMGSQVIIPYRCDTYDIMHLRPMGDLGQLLFLEWDARDKDSIRRVVQHSNVVINLIGRDWE
          G..VVNHLGR.GSQVIIPYRCDT.DIMHLRPMGDLG.LLFLEWDARDKDSI..VV.HSNVVINL.GRDWE
Retrocopy G*CVVNHLGRVGSQVIIPYRCDTCDIMHLRPMGDLG*LLFLEWDARDKDSIQ*VVEHSNVVINLVGRDWE

Parental  TSKLNFETGFYPYPKQLAQLSKEAGVEKFIHVSHLNARVDKCIHILRNKAVGEKVVRDAFPEAIIIKPSD
          T....FE..F...P...AQ.SKEAGV.KFIHV.HLN.........LRNKAVGEK..RDAFPEAII.K..D
Retrocopy TKNFDFEDVFVKIPQAIAQVSKEAGVGKFIHVAHLNVNIKSSSRYLRNKAVGEKAMRDAFPEAIIVKLLD

Parental  IFGREDRFLNSFASMHRFGPTPLGSLGWKTVKQPVYVVDVSKGIVNAVKDPDANGKSFAFVGPNRYLLFH
          I.GREDRFLN.FA.M..FG..PL.SLGWK.VKQPVYVVDVSKGIVNAVK.PDANGK.FAFVGPNRYLLF.
Retrocopy ICGREDRFLNYFANMCWFGAIPLVSLGWKAVKQPVYVVDVSKGIVNAVKEPDANGKTFAFVGPNRYLLFD

Parental  LVKYIFAVAHRLFLPFPLPLFAYRWVARVFEISPFEPWITRDKVERMHITDMKLPHLPGLEDLGIQATPL
          LVKYIFAVAHRLFLP.PLP.FAY.WVAR.FEIS.FE.W.TR.KVER.HIT.M.L.HLP.LEDLGIQATPL
Retrocopy LVKYIFAVAHRLFLPYPLPPFAYQWVARDFEISLFESWTTRNKVERIHITGMTLSHLPSLEDLGIQATPL

Parental  ELKAIEVLRRHRTYRWLSAEIEDVKPAKTVNI
          ELKAIEVL..H.TY.WLSAEIEDVKPAKTVNI
Retrocopy ELKAIEVLWLHHTYFWLSAEIEDVKPAKTVNI

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	2.05 RPM	45.01 RPM
SRP007412_cerebellum	3.40 RPM	59.58 RPM
SRP007412_heart	4.37 RPM	102.02 RPM
SRP007412_kidney	2.15 RPM	48.69 RPM
SRP007412_liver	1.44 RPM	28.55 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1905 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1905 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1905 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2585
Pan troglodytes	retro_ptro_1511
Gorilla gorilla	retro_ggor_1618
Macaca mulatta	retro_mmul_648

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000009588	1 retrocopy	retro_acar_16,
Danio rerio	ENSDARG00000070723	1 retrocopy	retro_drer_1,
Homo sapiens	ENSG00000139180	1 retrocopy	retro_hsap_2585,
Gorilla gorilla	ENSGGOG00000006076	1 retrocopy	retro_ggor_1618,
Macaca mulatta	ENSMMUG00000020813	1 retrocopy	retro_mmul_648,
Monodelphis domestica	ENSMODG00000018283	1 retrocopy	retro_mdom_209,
Nomascus leucogenys	ENSNLEG00000003252	1 retrocopy	retro_nleu_1520,
Otolemur garnettii	ENSOGAG00000005225	1 retrocopy	retro_ogar_2244,
Pongo abelii	ENSPPYG00000004171	1 retrocopy	retro_pabe_1905 ,
Pan troglodytes	ENSPTRG00000004557	1 retrocopy	retro_ptro_1511,
Ictidomys tridecemlineatus	ENSSTOG00000006504	1 retrocopy	retro_itri_543,