RetrogeneDB ID: retro_pabe_2225

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:76164385..76165066(+)
• Located in intron of: ENSPPYG00000013726

Retrocopy information

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

Parental gene information

• Parental gene symbol: H1FOO
• Ensembl ID: ENSPPYG00000013414
• Aliases: None
• Description: H1 histone family, member O, oocyte-specific [Source:HGNC Symbol;Acc:18463]

Sequence

>retro_pabe_2225
TATCCCCCCACTCTCCGCACGGTGGTAGAGGCGCTGCAGGCAGGGGAGTAGCGCTGGGGCATGTTGGCAATGGCCATCAA
GCTCTATATCCTGTACAAGTACCCAACGGTGGATGTCCTCTACTTCAAGTACCTGCTGAAGCAGGCGCTGGCCACTGGCA
TGTGCCACAGCCTCCTCGCCAGGCCCCTCAACTCCAAAGCCAGGGGGGCCACTGACAGCTTCAAATTAGATCCCAAGCAC
AAGAGGAAAATCCAGCCCAGGGAGATGGCCCCCTGATGGTCCCCAGGAGAGCAGGAGAGGCCAAGGGGAAGGACCCCAAG
AAAACAAGTGAGGCCAAGGAGGATCCTCCCAACGCGGGCAAGGTGAAGAAGGCAGCCAAGAGGCCAGCAGAGGTGCAGAA
GGCTCCTTCCAAGCCAGGTGCAGCCACAGAGAAGGTCGGCAAGCAAGGCAGTGCGGCCAAGGACACCAGGCCACAGCCGG
GTGAGGCTAGGAAGGCACCCCTAAGCCAGACAAGGCCACGCAGGCCTCTTCCAGTGCCAGCGGGCTCAGTAGGAAGGCAA
AGGCCAGAGGCAGCAGGAGCAGCCGAGATGTGAGGACCACAGGAAAATGAAAGCTGGGAGTAAGAGTTCAAAACCCACTG
TCAGCAAGGTCAAGAATGGTGTTGCTTCCTCGACCAGAAGG

Alignment

ORF - retro_pabe_2225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.55 %
• Parental protein coverage: 68.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HPPVLRMVLEALQAGEQRRGTSVAAIKLYILHKYPTVDVLRFKYLLKQALATGMRRGLLARPLNSKARGA
          .PP.LR.V.EALQAGE.R.G....AIKLYIL.KYPTVDVL.FKYLLKQALATGM...LLARPLNSKARGA
Retrocopy YPPTLRTVVEALQAGE*RWGMLAMAIKLYILYKYPTVDVLYFKYLLKQALATGMCHSLLARPLNSKARGA

Parental  TGSFKLVPKHKGKIQPRKMA-PPTAPRRAGEAKGKGPKKPSEAKEDPPNVGKVKKAAKRPAKVQKAPPKP
          T.SFKL.PKHK.KIQPR.MA.P...PRRAGEAKGK.PKK.SEAKEDPPN.GKVKKAAKRPA.VQKAP.KP
Retrocopy TDSFKLDPKHKRKIQPREMA<PLMVPRRAGEAKGKDPKKTSEAKEDPPNAGKVKKAAKRPAEVQKAPSKP

Parental  GAATEKPRKQGGAAKDTRAQSGEARKVP-PKPDKAMRAPSSTGRLSRKAKAKGSRSSQGDAEAYRRTKAE
          GAATEK..KQG.AAKDTR.Q.GEARK.P.PKPDKA..A.SS...LSRKAKA.GSRSS..D.......K..
Retrocopy GAATEKVGKQGSAAKDTRPQPGEARKAP<PKPDKATQASSSASGLSRKAKARGSRSSR-DVRTTGK*KLG

Parental  SKSSKPTAS-KVKNGAASPTKK
          .....P....KVKNG.AS.T..
Retrocopy VRVQNPLSA<KVKNGVASSTRR

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.18 RPM	0.00 RPM
SRP007412_kidney	0.03 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2225 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2225 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2225 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2799
Pan troglodytes	retro_ptro_1896
Gorilla gorilla	retro_ggor_1946

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017209	2 retrocopies	retro_cjac_3976, retro_cjac_981,
Felis catus	ENSFCAG00000000094	2 retrocopies	retro_fcat_1139, retro_fcat_416,
Homo sapiens	ENSG00000178804	1 retrocopy	retro_hsap_2799,
Gorilla gorilla	ENSGGOG00000000735	1 retrocopy	retro_ggor_1946,
Myotis lucifugus	ENSMLUG00000025226	2 retrocopies	retro_mluc_1278, retro_mluc_1318,
Oryctolagus cuniculus	ENSOCUG00000029379	1 retrocopy	retro_ocun_1483,
Ochotona princeps	ENSOPRG00000010371	2 retrocopies	retro_opri_403, retro_opri_624,
Pongo abelii	ENSPPYG00000013414	1 retrocopy	retro_pabe_2225 ,
Pan troglodytes	ENSPTRG00000015380	1 retrocopy	retro_ptro_1896,
Pteropus vampyrus	ENSPVAG00000007110	1 retrocopy	retro_pvam_808,
Tursiops truncatus	ENSTTRG00000011276	1 retrocopy	retro_ttru_1111,