RetrogeneDB ID: retro_pabe_1092

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:19300561..19301025(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB7
• Ensembl ID: ENSPPYG00000019596
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 7 [Source:HGNC Symbol;Acc:9544]

Sequence

>retro_pabe_1092
TCCAACTTGGAGCTCCACTCCATCTCTAGTGGCCATCTTCCTGAGTTGTCATGGCCAATCAGATACTGAAGCAAATGCTT
TTAAAGTATCAAGGTTACATTGGTGCAGCCCTAGTTTTAAGGAGATTGAGAATTTTTACTGGACCTCACCTCTACAGCAT
CTATCCTCATGAATCAACTGATAACTTGCCTCATCACCATGGATCCTCAGCAGCAAAGGCTGTATTTGAAGATATTCTAG
GCCAGATATGGGGAAAGAGGAAGCAAAGAAGATGGTGAATGAAGCCACTGCAGCTGGCTTCTTCAACAACCTGGGCTCTG
GAAGCCACATTGATCTCAGCATTATAGGAAAGAGCAAGGTAGATTTTCTTGGCCCATTCACAGTGCCCAAAAAGAAGGGG
ACTAGATTTGGCAGGTACAGGTGTGAGAAAAGGGACCACTGCAGTCCTCACCAAAGAAGCCACT

Alignment

ORF - retro_pabe_1092 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.94 %
• Parental protein coverage: 56.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SNLELHSLSTGRLPR-VVTANRMLKQMLFRYQGYIGAALVLGGVDV-TGPHLYSIYPHGSTDKLPYVTMG
          SNLELHS.S.G.LP..VV.AN..LKQML..YQGYIGAALVL......TGPHLYSIYPH.STD.LP.....
Retrocopy SNLELHSISSGHLPE<VVMANQILKQMLLKYQGYIGAALVLRRLRIFTGPHLYSIYPHESTDNLPH---H

Parental  SGSLAAMAVFEDKF-RPDMEEEEAKKLVSEAIAAGIFNDLGSGSNIDLCVISKNKLDFLRPYTVPNKKGT
          .GS.AA.AVFED...RPDM..EEAKK.V.EA.AAG.FN.LGSGS.IDL..I.K.K.DFL.P.TVP.KKGT
Retrocopy HGSSAAKAVFEDIL<RPDMGKEEAKKMVNEATAAGFFNNLGSGSHIDLSIIGKSKVDFLGPFTVPKKKGT

Parental  RLGRYRCEK-GTTAVLTEKIT
          R.GRYRCEK.GTTAVLT...T
Retrocopy RFGRYRCEK>GTTAVLTKEAT

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	69.50 RPM
SRP007412_cerebellum	0.00 RPM	53.02 RPM
SRP007412_heart	0.00 RPM	42.51 RPM
SRP007412_kidney	0.00 RPM	56.88 RPM
SRP007412_liver	0.00 RPM	49.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1092 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1092 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1092 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003067	2 retrocopies	retro_btau_1722, retro_btau_983,
Echinops telfairi	ENSETEG00000005432	2 retrocopies	retro_etel_2093, retro_etel_231,
Homo sapiens	ENSG00000136930	1 retrocopy	retro_hsap_1303,
Gorilla gorilla	ENSGGOG00000012164	1 retrocopy	retro_ggor_1019,
Nomascus leucogenys	ENSNLEG00000017268	1 retrocopy	retro_nleu_2947,
Otolemur garnettii	ENSOGAG00000003513	1 retrocopy	retro_ogar_2828,
Pongo abelii	ENSPPYG00000019596	1 retrocopy	retro_pabe_1092 ,
Pan troglodytes	ENSPTRG00000021354	1 retrocopy	retro_ptro_893,
Pteropus vampyrus	ENSPVAG00000000204	2 retrocopies	retro_pvam_1271, retro_pvam_866,
Rattus norvegicus	ENSRNOG00000011732	3 retrocopies	retro_rnor_1581, retro_rnor_1582, retro_rnor_2469,
Sorex araneus	ENSSARG00000009395	1 retrocopy	retro_sara_532,
Tupaia belangeri	ENSTBEG00000009196	2 retrocopies	retro_tbel_2889, retro_tbel_751,