RetrogeneDB ID: retro_pabe_1527

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17_random:7876668..7877827(+)
• Located in intron of: ENSPPYG00000008846

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000018452
• Aliases: None
• Description: None

Sequence

>retro_pabe_1527
ATGAGGTGGGTGGCCCTGTTCCTGAACGGCAGCCCCAAGAACGGAAAGGTGGTTGCTATATGTGGAACTTTATCTGATTT
GCTTTCTGTGGCCAGCAGTAAACTCGGCATCAAAGCCACCAGTGTGTATAATGGGAAAGGTGGACTGATTGATGATACTG
CTTTGATCAGGGATGATGATGTTTTGTTTGTGTGTGAAGGAGAGCCATTTATTGATCCTCAGACAGATTCTAAACCACCT
GAGGGATTGTCAGGATTCCACACAGACAGGCTAACATTAAATGTTGGAGGGCGGTACTTTACAACCACACAGAGCACTTT
AGTGAATAAAGAACCTGATAGTATCTGGCCCACATGTTTAAGGACAAAGATGTCTGGGAAATAAGCAAGATCACAGAGGA
GCTTTCTTAATTGACCGAAGTCCTGAGTACTTTGAACCCATTTTGAACTGCTTGCGTCATGGACAGCTTATTATAAATGA
TGGCATTAATTTATTGGATATGTTAGAAGAAGCAAGATTTTTTGGTATTGACTCATTGATTGAACACCTAGAAGTGGCAA
TAAAGAATGGCCCACCGGAGGATCATTCACCAATACCCTGAAAGGAATTTGTCTGATTTTTGCTAGCAACTCCAATCAAG
TCAGAACTGCGATGCCAAGGTTTGAACTTCAGTGGTGCTGATCTTTCTCATTTGGACCTTTGATACATTAACTTCAGAAT
GGCCAGTTTAAGCCGCTGCAATCTTGCACATGCAAATCTTTGCTGTGCAAATCTTAAACAAGCTGATCTCTCTGGATCAG
GGCGTGACTGTGCAAATCTCCAGGGAGTCAAGATGGTCTGTTCTAATGTAGAAGGAGCATCCCTGAAACTGTGTAATTTT
GAGTATCCTTCTGGTCTTAAAGCCAGTTTAGAAGATGCTAACCTGAAAGGTGTGGATATGGAAGGAAGTCAGATAACAGG
AATTAACCTGAGAGTGACTACCTTAAATGCAAAGTTGAAGAACTGTAACCTCAGAGGAGCAACTCTGGCAGGAACTGATT
TAGAGAATTATGATCTGTCTGGGTGTGATCTTCAAGAAGCCAACCTGAGAAGGTCCAACATGAAGGGAGCTAGATTTGAA
GAGATGCTGACACCACTACACATGTCACAAAGTGTTAGA

Alignment

ORF - retro_pabe_1527 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRRVTLFLNGSPKNGKVVAVYGTLSDLLSVASSKLGIKATSVYNGKGGLIDDIALIRDDDVLFVCEGEPF
          MR.V.LFLNGSPKNGKVVA..GTLSDLLSVASSKLGIKATSVYNGKGGLIDD.ALIRDDDVLFVCEGEPF
Retrocopy MRWVALFLNGSPKNGKVVAICGTLSDLLSVASSKLGIKATSVYNGKGGLIDDTALIRDDDVLFVCEGEPF

Parental  IDPQTDSKPPEGLLGFHTDWLTLNVGGRYFTTTRSTLVNKEPDSM-LAHMFKDKGVW-GNKQDHRGAFLI
          IDPQTDSKPPEGL.GFHTD.LTLNVGGRYFTTT.STLVNKEPDS..LAHMFKDK.VW.GNKQDHRGAFLI
Retrocopy IDPQTDSKPPEGLSGFHTDRLTLNVGGRYFTTTQSTLVNKEPDSI<LAHMFKDKDVW<GNKQDHRGAFLI

Parental  DRSPEYFEPILNYLRHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQPPEDHSPISRKEFVRF
          DRSPEYFEPILN.LRHGQLI.NDGINLL..LEEARFFGIDSLIEHLEVAIKN..PPEDHSPI..KEFV.F
Retrocopy DRSPEYFEPILNCLRHGQLIINDGINLLDMLEEARFFGIDSLIEHLEVAIKNG-PPEDHSPIP*KEFV*F

Parental  LLATPTKSELRCQGLNFSGADLSRLDLRYINFKMANLSRCNLAHANLCCANLERADLSGSVLDCANLQGV
          LLATP.KSELRCQGLNFSGADLS.LDL.YINF.MA.LSRCNLAHANLCCANL..ADLSGS..DCANLQGV
Retrocopy LLATPIKSELRCQGLNFSGADLSHLDL*YINFRMASLSRCNLAHANLCCANLKQADLSGSGRDCANLQGV

Parental  KMLCSNAEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQMTGINLRVATLKNAKLKNCNLRGATLAGT
          KM.CSN.EGASLKLCNFE.PSGLKA.LE.ANLKGVDMEGSQ.TGINLRV.TL.NAKLKNCNLRGATLAGT
Retrocopy KMVCSNVEGASLKLCNFEYPSGLKASLEDANLKGVDMEGSQITGINLRVTTL-NAKLKNCNLRGATLAGT

Parental  DLENCDLSGCDLQEANLRGSNVKGAIFEEMLTPLHMSQSVR
          DLEN.DLSGCDLQEANLR.SN.KGA.FEEMLTPLHMSQSVR
Retrocopy DLENYDLSGCDLQEANLRRSNMKGARFEEMLTPLHMSQSVR

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	0.33 RPM	5.58 RPM
SRP007412_cerebellum	0.61 RPM	11.19 RPM
SRP007412_heart	0.21 RPM	14.33 RPM
SRP007412_kidney	0.10 RPM	10.61 RPM
SRP007412_liver	0.06 RPM	5.57 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1527 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1527 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1527 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1730

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012157	1 retrocopy	retro_chof_323,
Gorilla gorilla	ENSGGOG00000004480	3 retrocopies	retro_ggor_1309, retro_ggor_2264, retro_ggor_2791,
Macaca mulatta	ENSMMUG00000010151	3 retrocopies	retro_mmul_1083, retro_mmul_1218, retro_mmul_2072,
Nomascus leucogenys	ENSNLEG00000016156	3 retrocopies	retro_nleu_1386, retro_nleu_2499, retro_nleu_2990,
Pongo abelii	ENSPPYG00000008616	1 retrocopy	retro_pabe_2093,
Pongo abelii	ENSPPYG00000018452	3 retrocopies	retro_pabe_1527 , retro_pabe_2725, retro_pabe_3457,