RetrogeneDB ID: retro_pabe_3027

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6_qbl_hap2:359434..360544(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP469E0314
• Ensembl ID: ENSPPYG00000002459
• Aliases: None
• Description: actin, aortic smooth muscle [Source:RefSeq peptide;Acc:NP_001126814]

Sequence

>retro_pabe_3027
GAAGGAGAGATCGCGGCGCTTGTCATTGACAATGGGTCCGGCATGTGCAAAGCTGGCTTTCCTAGGAATGACGCCCCCGA
GCCATGTTTTCCTCCATCTTTGGGCGCCTCCGGCACCAGAGCATAATGGTGGGCATGGGCCAGGACTCCCACATGGGCGA
TGAGGCCCAGAGCAAGCAAGGCATCCTGACCCTGAAGTATCCCATTGAGCATGACATCATCACCAACTGGGACGACATGG
AGATCTGGCACCTCACCTTCTACAACAAGCTGTGCATGGCCCCAGAGGAGCACCCGGTGCTGTTGACCATGGCTCCCCTG
AACCCCAAGGCCAACAGAGAGAAGATGACTCATCATGTTCGAGACCTTCAATACTCGGGCCATATACATGGCTATCCAGG
CCGTGCTGTCCCTCTACACCTCTCGGCGAACCACTGGCATTGTCATGGACTCTGGAGACTGGGTCATACACATGGTGCCC
ATCTATGAGGGCTATGCCCTCCCCCACACCATCCTGTGTCTGGACCTGGCTGGCTGGGACCTGACCCACTACCTCATGAA
GATTCTCACCGAGTGTGGCTACAGCTTCATCACCATGGCTGAGTGGGAGATCATGCGCGACGTCAAGGAGAAGCTGTGCT
ACGTTGCCCTAGACTTCTAGCAGGAGATGGCCATGCTGCATCCTCCTCTTCCCTGGAGAAGAGCTACAAGCTGCCCAATG
GTCAGATCATCACAATCTGCAATGAGTGGCTTCAGTATCCGGAGGCACTGTTCCAGCCTTCCTTCCTGGGCATGGAATCT
TGCGGCATCCACGAGACCACCATCAACTCCTTCATGAAGTACGAGGTGGACATCTGCAAAGACCTGTGCCAACACGGTGC
TGTCAGGTGGCACCACCATGTACCCGGGCATCGCCAACAGGATGCAGAAGGAGATCCCTGCCCTGGCACCCAGCACCATG
AAGATCAAGATCGTTGCACCCCCAGAGCACAAGTACTCGGTGTGGATCGGCGGCTCCATCCTGGCCTCACTGTCCACCTT
CCAGCAGATATGGATTAGCAAGCAGGAGTACCACGAGTCCGGCCCCTCCATCATCCACTGCAAATGCTTC

Alignment

ORF - retro_pabe_3027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.81 %
• Parental protein coverage: 99.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EEDSTALVCDNGSGLCKAGFAGDDAP-RAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
          E....ALV.DNGSG.CKAGF...DAP.RA.F.SI.GR.RHQ..MVGMGQ.DS..GDEAQSK.GILTLKYP
Retrocopy EGEIAALVIDNGSGMCKAGFPRNDAP<RAMFSSIFGRLRHQSIMVGMGQ-DSHMGDEAQSKQGILTLKYP

Parental  IEHGIITNWDDMEKIWHHSFYNELRVAPEEHPTLLTEAPLN-PKANREKMTQIMFETFNVPAMYVAIQAV
          IEH.IITNWDDME.IWH..FYN.L..APEEHP.LLT.APLN.P....E....IMFETFN..A.Y.AIQAV
Retrocopy IEHDIITNWDDME-IWHLTFYNKLCMAPEEHPVLLTMAPLN>PRPT-ERR*LIMFETFNTRAIYMAIQAV

Parental  LSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIV
          LSLY.S.RTTGIV.DSGD.V.H.VPIYEGYALPH.I..LDLAG.DLT.YLMKILTE.GYSF.T.AE.EI.
Retrocopy LSLYTSRRTTGIVMDSGDWVIHMVPIYEGYALPHTILCLDLAGWDLTHYLMKILTECGYSFITMAEWEIM

Parental  RDIKEKLCYVALDFENEMAT-AASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETT
          RD.KEKLCYVALDF..EMA..AASSSSLEKSY.LP.GQ.ITI.NE....PE.LFQPSF.GMES.GIHETT
Retrocopy RDVKEKLCYVALDF*QEMAM<AASSSSLEKSYKLPNGQIITICNEWLQYPEALFQPSFLGMESCGIHETT

Parental  YNSIMKCDIDIRKDLYANNVL-SGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILA
          .NS.MK...DI.KDL........G.T.MYPGIA.RMQKEI.ALAPSTMKIKI.APPE.KYSVWIGGSILA
Retrocopy INSFMKYEVDICKDLCQHGAV>GGTT-MYPGIANRMQKEIPALAPSTMKIKIVAPPEHKYSVWIGGSILA

Parental  SLSTFQQMWISKQEYDEAGPSIVHRKCF
          SLSTFQQ.WISKQEY.E.GPSI.H.KCF
Retrocopy SLSTFQQIWISKQEYHESGPSIIHCKCF

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	70.72 RPM
SRP007412_cerebellum	0.00 RPM	7.66 RPM
SRP007412_heart	0.00 RPM	52.26 RPM
SRP007412_kidney	0.00 RPM	195.96 RPM
SRP007412_liver	0.00 RPM	205.55 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3027 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3027 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3027 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 62 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000759	3 retrocopies	retro_chof_1909, retro_chof_2042, retro_chof_21,
Dasypus novemcinctus	ENSDNOG00000006719	1 retrocopy	retro_dnov_32,
Echinops telfairi	ENSETEG00000008526	1 retrocopy	retro_etel_41,
Macropus eugenii	ENSMEUG00000010843	1 retrocopy	retro_meug_1374,
Myotis lucifugus	ENSMLUG00000015509	3 retrocopies	retro_mluc_190, retro_mluc_427, retro_mluc_90,
Nomascus leucogenys	ENSNLEG00000012233	1 retrocopy	retro_nleu_2313,
Oryctolagus cuniculus	ENSOCUG00000008193	3 retrocopies	retro_ocun_1306, retro_ocun_1421, retro_ocun_919,
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,
Sorex araneus	ENSSARG00000005778	1 retrocopy	retro_sara_732,
Tupaia belangeri	ENSTBEG00000017616	3 retrocopies	retro_tbel_1555, retro_tbel_3014, retro_tbel_4616,
Tarsius syrichta	ENSTSYG00000008155	5 retrocopies	retro_tsyr_1282, retro_tsyr_2102, retro_tsyr_858, retro_tsyr_9, retro_tsyr_92,
Vicugna pacos	ENSVPAG00000010621	3 retrocopies	retro_vpac_12, retro_vpac_355, retro_vpac_651,