RetrogeneDB ID: retro_pabe_1930

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:18476599..18477555(+)
• Located in intron of: ENSPPYG00000012151

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTR1A
• Ensembl ID: ENSPPYG00000002605
• Aliases: None
• Description: ARP1 actin-related protein 1 homolog A, centractin alpha (yeast) [Source:HGNC Symbol;Acc:167]

Sequence

>retro_pabe_1930
ATGGAGTCCTACGATGTGATCACCAACCAACCTGTCATGATCGACAATGGATCTCGTGTGATTAAAGCTGGTTTTGCTGG
CGATCAGATCCCCAAATACTGCTTTCCAAAGTATGTGGGCCTACCCTTGCACATTCGTATCATGGCAGGAGCCCTTGAAG
GTGACATCTTCATTGGCTTCAAAGCCAAGGAGCACCAAGGGCTGCTCTCGATCTGCTATCTCATGGAGCATGGCATTGTC
AAGGACTGGAATGACATGGAACACATCTGGCAATATGTCTATTCTAAGGACCAGCTGCAGACTTTCTCAGAGGAGCATCT
TGCGCTCCTCACTGAGGTGCCTTTAAACCCACAAAGACACCAGGAACGAGCTGCCAACGTTTTCTTCAAGAGCTTCAATG
TGCCTGCTATTTTGATCTCCATGTAAGCTGTGCTCAGCCTTTATGCCACAGGCAGGACCACAGGGGTGGTGCTGGATTCT
GGGGATGGCATCACCCATGCTGTGCCCATCTATGAGGGTTTTGCCATGCTCACTCCATCATGTGCATTGACACCGCAGGC
CAGGACATCTCTCGTTTCCTGCACCTCTACCTGCATAAGGAGGGCTACAATTTCCACTTATCCTCCGAGTTTGAGATTGT
CAAGGCCATAAAAGAAAGACCCTCCTACCTATTCATAAACCCCCAGAAGGAAGAGACACTAGAGACAGGGAAGGCTCAGT
ACTACCTGCCTGATGGCAGCACCATTGAGATTGGTCCTTCCCAATTCCGGGCCCCTGAGCTGTTCTTCAGGCCAGACTTG
ATCAGGGAGGAGAGTGAAAGCATTCACAAGGTCCTGGTGTTCGCCATCCAGAAGTCAGACACAGACCTGCAGCTCATGCT
TTTCTCCAACATCGTCCTCTTGGGAGGCTCTACCTTGTTCAAAGGTTTTGGTGACAGGCTACTGAGTGAAGTGAAG

Alignment

ORF - retro_pabe_1930 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.44 %
• Parental protein coverage: 84.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MESYDVIANQPVVIDNGSGVIKAGFAGDQIPKYCFPNYVGRPKHVRVMAGALEGDIFIGPKAEEHRGLLS
          MESYDVI.NQPV.IDNGS.VIKAGFAGDQIPKYCFP.YVG.P.H.R.MAGALEGDIFIG.KA.EH.GLLS
Retrocopy MESYDVITNQPVMIDNGSRVIKAGFAGDQIPKYCFPKYVGLPLHIRIMAGALEGDIFIGFKAKEHQGLLS

Parental  IRYPMEHGIVKDWNDMERIWQYVYSKDQLQTFSEEHPVLLTEAPLNPRKNRERAAEVFFETFNVPALFIS
          I.Y.MEHGIVKDWNDME.IWQYVYSKDQLQTFSEEH..LLTE.PLNP....ERAA.VFF..FNVPA..IS
Retrocopy ICYLMEHGIVKDWNDMEHIWQYVYSKDQLQTFSEEHLALLTEVPLNPQRHQERAANVFFKSFNVPAILIS

Parental  MQAVLSLYATGRTTGVVLDSGDGVTHAVPIYEGFAM-PHSIMRIDIAGRDVSRFLRLYLRKEGYDFHSSS
          M.AVLSLYATGRTTGVVLDSGDG.THAVPIYEGFAM..HSIM.ID.AG.D.SRFL.LYL.KEGY.FH.SS
Retrocopy M*AVLSLYATGRTTGVVLDSGDGITHAVPIYEGFAM<AHSIMCIDTAGQDISRFLHLYLHKEGYNFHLSS

Parental  EFEIVKAIKERACYLSINPQKDETLETEKAQYYLPDGSTIEIGPSRFRAPELLFRPDLIGEESEGIHEVL
          EFEIVKAIKER..YL.INPQK.ETLET.KAQYYLPDGSTIEIGPS.FRAPEL.FRPDLI.EESE.IH.VL
Retrocopy EFEIVKAIKERPSYLFINPQKEETLETGKAQYYLPDGSTIEIGPSQFRAPELFFRPDLIREESESIHKVL

Parental  VFAIQKSDMDLRRTLFSNIVLSGGSTLFKGFGDRLLSEVK
          VFAIQKSD.DL...LFSNIVL.GGSTLFKGFGDRLLSEVK
Retrocopy VFAIQKSDTDLQLMLFSNIVLLGGSTLFKGFGDRLLSEVK

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	145.08 RPM
SRP007412_cerebellum	0.12 RPM	95.70 RPM
SRP007412_heart	0.06 RPM	31.28 RPM
SRP007412_kidney	0.10 RPM	67.35 RPM
SRP007412_liver	0.03 RPM	31.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1930 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1930 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1930 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2141
Pan troglodytes	retro_ptro_1567

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000138107	1 retrocopy	retro_hsap_2141,
Mus musculus	ENSMUSG00000025228	1 retrocopy	retro_mmus_2686,
Nomascus leucogenys	ENSNLEG00000015157	1 retrocopy	retro_nleu_2751,
Pongo abelii	ENSPPYG00000002459	1 retrocopy	retro_pabe_3027,
Pongo abelii	ENSPPYG00000002605	1 retrocopy	retro_pabe_1930 ,
Pongo abelii	ENSPPYG00000006318	1 retrocopy	retro_pabe_1317,
Pongo abelii	ENSPPYG00000008735	11 retrocopies	retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pongo abelii	ENSPPYG00000017336	23 retrocopies	retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Pan troglodytes	ENSPTRG00000002894	1 retrocopy	retro_ptro_1567,
Drosophila melanogaster	FBgn0011745	1 retrocopy	retro_dmel_80,