RetrogeneDB ID: retro_pabe_2208

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:32291035..32292210(+)
• Located in intron of: ENSPPYG00000013596

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM175A
• Ensembl ID: ENSPPYG00000014898
• Aliases: None
• Description: family with sequence similarity 175, member A [Source:HGNC Symbol;Acc:25829]

Sequence

>retro_pabe_2208
GTGTTCTCGGGCTTTGTGTTGACCAGCTTGCCTTACACAACCCCAGCACTGTCTGGGACACGGAAGGTTTTCTTCTTGAG
GAAGTAAAAGATGAAGCCAAGAATAGCATTACTGATTCCCAAATGGATGATGTTGAAGTTGTTTATACAATTGACATTCA
GAAATATATTCCATGCTTTTTTAGCTTTTATAATTCCTCAAGTGAAGTAAATGAGCAAGCACTGAAGAAAATATTCTCCA
ATGTCAAAAAGAATGTGATAGGTTGGTACAAATTCTGTCGTCATTCAGATCAGATCATGACGTTTAGAGAGAGGCTGCTT
CACAAAAACTTGCAGGAGCATTTTTCAAACCAATAACTTATTTTTCTACTATTAACACCAAGTATAATAACAGAAAGCTG
TTCTACTCATCGACTGAAACATGCCTTGAAACCTCAAAAAGGACTTTCTCACAGGGTACTTTTAGTGGTTGCCAATCTGG
GTATTTCTGAACAACTAGGTTATAAAACTGTATCAGGTTCCTGTACATCCACTGGTTTTAGCCAAGCAGTAAAAACACAC
AGCTCTAAATTTTTTGAAGAAGATGGATCATTAAAGGAGGTACATAAGATAAATGAAATGTAATGCTTCATTACAAGAGG
AATTAAAGAGTATATGCAAAAAAAAGTGGAAGACAATGAACAAGCAATAAATAAACTAGTAAAGGATATAAACAGATTAA
AACAAGAAATTGGAAAAAAGGAGATGAGCATAGATTCAGGCAGCCTGAGAGAAGAACATCTAAAAAGACCCTCAGGGGAA
CATTTTTCCTGGTCAAGCATTATGGACCTTTTATCCAGATTCTGAATTTCTTCATTCGTATGTTGTCTTTTAAAAAAACA
GACATGTTTCTAAAAGCTGTAACAACAACCTCCACTTCGATGTGGTAGCCAATCTGACCTTAATGGTAGAACACACTGAC
ATTCCTGAAGCTAGTCTAGCTAGTAGACCACAAATGACTAAGCATAAAGCCTTAGACTTAGATGACAGATGACAATTCAA
GAAATCGCAGCAGTTAGAGATACAAGACAAACCATCTAAAACAGATACTGGTAGTAGTAACCAAGAAAAGCATCTACAAT
GAGCAGCCCAGAAATAGATGAAGAGATTGAGAAAATGAAGGGATCTAGTGAATAT

Alignment

ORF - retro_pabe_2208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.94 %
• Parental protein coverage: 96.58 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLSGFVLGAL-AFQHLNTDSDTEGFLLGEVKGEAKNSITDSQMDDVEVVYTIDIQKYIPCYQLFSFYNSS
          V.SGFVL..L.A.....T..DTEGFLL.EVK.EAKNSITDSQMDDVEVVYTIDIQKYIPC...FSFYNSS
Retrocopy VFSGFVLTSL<ALHNPSTVWDTEGFLLEEVKDEAKNSITDSQMDDVEVVYTIDIQKYIPCF--FSFYNSS

Parental  GEVNEQALKKILSNVKKNVVGWYKFRRHSDQIMTFRERLLHKNLQEHFSNQDLVFLLLTPSIITESCSTH
          .EVNEQALKKI.SNVKKNV.GWYKF.RHSDQIMTFRERLLHKNLQEHFSNQ.L.FLLLTPSIITESCSTH
Retrocopy SEVNEQALKKIFSNVKKNVIGWYKFCRHSDQIMTFRERLLHKNLQEHFSNQ*LIFLLLTPSIITESCSTH

Parental  RLEHSLYKPQKGLFHRVPLVVANLGMSEQLGYKTVSGSCMSTGFSRAVQTHSSKFFEEDGSLKEVHKINE
          RL.H.L.KPQKGL.HRV.LVVANLG.SEQLGYKTVSGSC.STGFS.AV.THSSKFFEEDGSLKEVHKINE
Retrocopy RLKHAL-KPQKGLSHRVLLVVANLGISEQLGYKTVSGSCTSTGFSQAVKTHSSKFFEEDGSLKEVHKINE

Parental  MYASLQEELKS-ICKKVEDSEQAVDKLVKDVNRLKREI-EKRRGAQIQAAREKNIQKDPQENIFLCQALR
          M........K......VED.EQA..KLVKD.NRLK.EI.EKRR.A.IQAA.EKNI.KDPQ.NIF..QAL.
Retrocopy M*CFITRGIKEYMXXXVEDNEQAINKLVKDINRLKQEI>EKRR*A*IQAA*EKNI*KDPQGNIFPGQALW

Parental  TFFPNSEFLHSCVMSLKNRHVSKSSCNYNHHLDVVDNLTLMVEHTDIPEASPASTPQIIKHKALDLDDRW
          TF.P.SEFLHS.V...KNRHVSKS.CN.N.H.DVV.NLTLMVEHTDIPEAS.AS.PQ..KHKALDLDDR.
Retrocopy TFYPDSEFLHSYVVF*KNRHVSKS-CNNNLHFDVVANLTLMVEHTDIPEASLASRPQMTKHKALDLDDR*

Parental  QFKRSRLLDTQDKRSKTDTDSSNQD-KASKMSSPETDEEIEKMKGFGEY
          QFK.S..L..QDK.SKTDT.SSNQ..KAS.MSSPE.DEEIEKMKG..EY
Retrocopy QFKKSQQLEIQDKPSKTDTGSSNQE<KASTMSSPEIDEEIEKMKGSSEY

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	4.15 RPM
SRP007412_cerebellum	0.00 RPM	7.17 RPM
SRP007412_heart	0.00 RPM	2.95 RPM
SRP007412_kidney	0.00 RPM	5.80 RPM
SRP007412_liver	0.00 RPM	3.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2208 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2208 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2208 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1911
Macaca mulatta	retro_mmul_1499

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013241	1 retrocopy	retro_chof_2580,
Homo sapiens	ENSG00000163322	1 retrocopy	retro_hsap_4024,
Macaca mulatta	ENSMMUG00000015357	2 retrocopies	retro_mmul_1499, retro_mmul_2320,
Nomascus leucogenys	ENSNLEG00000009133	2 retrocopies	retro_nleu_1198, retro_nleu_661,
Pongo abelii	ENSPPYG00000014898	2 retrocopies	retro_pabe_2208 , retro_pabe_3301,
Pan troglodytes	ENSPTRG00000023645	2 retrocopies	retro_ptro_1911, retro_ptro_2728,