RetrogeneDB ID: retro_pabe_3301

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:17485329..17486155(-)
• Located in intron of: None

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_3301
CTGAAGAAAATATTATCAAATTCACAAAGAATGTGGTAGGTTGGTACAAATTCCGTCGTCATTCAGATCAGATCATGACA
TTTAGAGACAGGCTGCTTCACAAAAGCTTGCAGGAGCATTTTTCAAACCAAGACCTTGTTTTTCTGCTATGAACACCAAG
TATAATAACAGAAAGCCGCTCTACTCATTGACTGGAACATGCCTTATATAAACCTCGAAAAGGACTTTTTCACAGGGTAC
CTTTAGTGGTTGCCAATCTGGGCATGTCTGAACAACTAGGTTATAAAACTGTATCAGGTTCCTGTATGTCCACTGGTTTT
AGCTGAGCTGTACAAACATACAGCTCTAAATTTTTTGAAGAAGATGGATCCTTAAAGGAGGTACATAAGATAAATGAAAT
GTATGCTTCATTGTAAGAGGAATTAAAGAGTATATGCAAAAAAGTGGAAGACAGTGAACAAGCAGTAGATAAACTAGTAA
AGGATGTAAACAGATTAAAACGAGAAATTGAAAAAAGGAGATGAGCCCAGATTCCGGCAGCACGAGAGAAGAGCATCCAA
AAAAGACCCTCAGGAGAACATTTTTCTTTGTCAAGAATTATGGACCTTTTTTCCAGATTCTGAATTTCTTCATTCATGTG
TTATGTCTTTAAAAAAATAGACATGTTTCTAAAGGTAGCTCTAACAACCACCACCATCTCGATGTAGTAGACAATCTGAC
CTTAATGGTAGAAAACACTGACATTCCTGAAGCTAGTCCAGCTAGTACACCACAAATGGTTAAGCATAAAACCTTAGACT
TAGCTGACAGATGGCAATTCAAGAGA

Alignment

ORF - retro_pabe_3301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.21 %
• Parental protein coverage: 67.24 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LKKILSNVK-KNVVGWYKFRRHSDQIMTFRERLLHKNLQEHFSNQDLVFLLLTPSIITESCSTHRLEHSL
          LKKILSN...KNVVGWYKFRRHSDQIMTFR.RLLHK.LQEHFSNQDLVFLL.TPSIITES.STH.LEH.L
Retrocopy LKKILSNSQ<KNVVGWYKFRRHSDQIMTFRDRLLHKSLQEHFSNQDLVFLL*TPSIITESRSTH*LEHAL

Parental  YKPQKGLFHRVPLVVANLGMSEQLGYKTVSGSCMSTGFSRAVQTHSSKFFEEDGSLKEVHKINEMYASLQ
          YKP.KGLFHRVPLVVANLGMSEQLGYKTVSGSCMSTGFS.AVQT.SSKFFEEDGSLKEVHKINEMYASL.
Retrocopy YKPRKGLFHRVPLVVANLGMSEQLGYKTVSGSCMSTGFS*AVQTYSSKFFEEDGSLKEVHKINEMYASL*

Parental  EELKSICKKVEDSEQAVDKLVKDVNRLKREIEKRRGAQIQAAREKNIQ-KDPQENIFLCQALRTFFPNSE
          EELKSICKKVEDSEQAVDKLVKDVNRLKREIEKRR.AQI.AAREK.IQ.KDPQENIFLCQ.L.TFFP.SE
Retrocopy EELKSICKKVEDSEQAVDKLVKDVNRLKREIEKRR*AQIPAAREKSIQ>KDPQENIFLCQELWTFFPDSE

Parental  FLHSCVMSL-KNRHVSKSSCNYNHHLDVVDNLTLMVEHTDIPEASPASTPQIIKHKALDLDDRWQFKR
          FLHSCVMSL.KNRHVSK.S.N..HHLDVVDNLTLMVE.TDIPEASPASTPQ..KHK.LDL.DRWQFKR
Retrocopy FLHSCVMSL>KNRHVSKGSSNNHHHLDVVDNLTLMVENTDIPEASPASTPQMVKHKTLDLADRWQFKR

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	0.12 RPM	7.17 RPM
SRP007412_heart	0.00 RPM	2.95 RPM
SRP007412_kidney	0.00 RPM	5.80 RPM
SRP007412_liver	0.03 RPM	3.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3301 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3301 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3301 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4024
Pan troglodytes	retro_ptro_2728

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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,