RetrogeneDB ID: retro_pabe_953

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:98965837..98966218(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAFAH1B2
• Ensembl ID: ENSPPYG00000003907
• Aliases: PAFAH1B2, PAFAHB
• Description: Platelet-activating factor acetylhydrolase IB subunit beta [Source:UniProtKB/Swiss-Prot;Acc:Q5R4G2]

Sequence

>retro_pabe_953
TGTAGAATGAGCCAAGCTGACTCAAACACAGCAGCTATTCCACATGCAGTAGAAGATATTCAAGGAGACGACAGATGGAT
ATCTCAGCACAACAGATTTGTCCTGGATGGTAAAGACAAAAAGCCTAGTGTTCTGTTTGTGGGAGACCCCATGGTGCAGT
TAATGCAGCAACACGAGATATGGCGAGAGCTTTTTTCCCCATTTCACGTACTGAATTTTGGAACTGAGGAAGATACAAGA
CACGTTTTGTAGAAACTAAAGAGTAGAGAACTGGAGAATATTAAACCTAAGGTCATTGTTGTCTGGGTAGGAACAAACAA
CCATGAAAATACAGCAGTAGAGTTAGGAGGTGGGATCAAGGCCATCATTCACTCTATCAAT

Alignment

ORF - retro_pabe_953 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.69 %
• Parental protein coverage: 53.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CRMSQGDSNPAAIPHAAEDIQGDDRWMSQHNRFVLDCKDKEPDVLFVGDSMVQLMQQYEIWRELFSPLHA
          CRMSQ.DSN.AAIPHA.EDIQGDDRW.SQHNRFVLD.KDK.P.VLFVGD.MVQLMQQ.EIWRELFSP.H.
Retrocopy CRMSQADSNTAAIPHAVEDIQGDDRWISQHNRFVLDGKDKKPSVLFVGDPMVQLMQQHEIWRELFSPFHV

Parental  LNFGIGGDTTRHVLWRLKNGELENIKPKVIVVWVGTNNHENTAEEVAGGIEAIVQLIN
          LNFG...D.TRHVL..LK..ELENIKPKVIVVWVGTNNHENTA.E..GGI.AI...IN
Retrocopy LNFGTEED-TRHVL*KLKSRELENIKPKVIVVWVGTNNHENTAVELGGGIKAIIHSIN

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	90.01 RPM
SRP007412_cerebellum	0.00 RPM	112.85 RPM
SRP007412_heart	0.00 RPM	31.28 RPM
SRP007412_kidney	0.00 RPM	37.09 RPM
SRP007412_liver	0.00 RPM	39.90 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_953 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_953 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_953 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1148
Pan troglodytes	retro_ptro_782
Gorilla gorilla	retro_ggor_893
Macaca mulatta	retro_mmul_892
Callithrix jacchus	retro_cjac_3325

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008628	2 retrocopies	retro_amel_1145, retro_amel_818,
Canis familiaris	ENSCAFG00000013226	1 retrocopy	retro_cfam_1335,
Callithrix jacchus	ENSCJAG00000012698	1 retrocopy	retro_cjac_3325,
Dipodomys ordii	ENSDORG00000011274	1 retrocopy	retro_dord_560,
Felis catus	ENSFCAG00000029945	1 retrocopy	retro_fcat_270,
Homo sapiens	ENSG00000168092	2 retrocopies	retro_hsap_1148, retro_hsap_4661,
Gorilla gorilla	ENSGGOG00000028197	2 retrocopies	retro_ggor_2893, retro_ggor_893,
Macaca mulatta	ENSMMUG00000002050	2 retrocopies	retro_mmul_2481, retro_mmul_892,
Mustela putorius furo	ENSMPUG00000004246	1 retrocopy	retro_mputfur_898,
Nomascus leucogenys	ENSNLEG00000007337	2 retrocopies	retro_nleu_1096, retro_nleu_946,
Pongo abelii	ENSPPYG00000003907	2 retrocopies	retro_pabe_3621, retro_pabe_953 ,
Pan troglodytes	ENSPTRG00000004318	2 retrocopies	retro_ptro_3097, retro_ptro_782,
Rattus norvegicus	ENSRNOG00000018032	1 retrocopy	retro_rnor_2585,
Sarcophilus harrisii	ENSSHAG00000011403	1 retrocopy	retro_shar_617,