RetrogeneDB ID: retro_pabe_613

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:89880432..89881459(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT9
• Ensembl ID: ENSPPYG00000014914
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 9 [Source:HGNC Symbol;Acc:8056]

Sequence

>retro_pabe_613
ATGGCTGGACGCCGCCTGTCCAAGGCTTTAGCGACCATGTCTCCCTTCATGACCTTGTCTCTGTGACAGGCAGGCCCGGC
AGCTGCCCCAACATCCCGGCCAGCTGGAGCCCGTTTTCCTCACATGGGTTTTCTCTAAATTTCATCATGTCAGTTTCGAA
GCGCACTGCTGAGAAGCTCCACGAGAAGGCCCGGACACCTCCGTACCCTGGCTCCAAGGTGGAGCGAAGCCTGGTTCCCC
ATGAGAAAGTGAGCTGGCTGGCCGAGTGGCGAGAGTAACGCCCGTGGAGTACACTGCCAGCTCTATCTTGCCTGGGCCCC
TGTGGGCAGACCCTCAAGTGGGTGAAAGGAACTTCTCTCCTAAGTTTAACGAAAAGGATGGGCATGTGGAGAGAAGGAAC
CAGCATGGCTTGTATGAAATTGAGAAGGGTAGACTTAGAAATCCTGCATCTCGGACAGGACTGGTTGGCCAAGGGCCTTT
GGGGTGTTGGGGCCCCAGTCATGCTGTAGATCCCATCTTAACTAGATGGAAAAGAGATAGCCGGGGAAACGAAATTACCC
CCCCTATTTCTGGGAAAAATATCCTGCAATTTGTAGCCATCTAAAGGAAGGACCATGGAGAATAGGCAATCCCAGGGGGG
ATGGTGGATCCAGGAGAGAAAATTAGCGCTACATTGAAGAGATAATTTGACGAGGAAGCCATGAACTCTTTACAGAAATC
TAGGAAAGAAATGCAGGAGTTGGAGAGACAATTGCACAAACTCCTCAGCCAGGAACATTTTGTGGTCTATAAAGGCTACG
TGGATGATTCTCGGAACACAGATAACTGCTGGATAAAGACAGAGGCTGTGAACTACCATGATGAAATAATGGACCATCTT
CCTCTGGAAGCTGGCAATGATGCCAAGAAAGTGAAATGGGTGGACATTAATGATAAACTTGAGCTTTATGCCAGCCACTC
CCAATTTATTCAACTTGTGGCTGAGAAACGAGATGCCCACTGAAGTGAGGATATGTATCCTGATTGT

Alignment

ORF - retro_pabe_613 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.34 %
• Parental protein coverage: 99.14 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGRLLGKALAAVSLSVALA-SVTIRPSGCRGIPAFRNSFSSSWFHLNTNVMSGSNGSKENSHNKARTSP
          MAGR.L.KALA..S....L..SVT.RP..C..IPA....FSS..F.LN...MS.S....E..H.KART.P
Retrocopy MAGRRLSKALATMSPFMTLS<SVTGRPGSCPNIPASWSPFSSHGFSLNF-IMSVSKRTAEKLHEKARTPP

Parental  YPGSKVERSQVPNEKVGWLVEWQD-YNPVEYTAVSVLAGPRWADPQISESNFSPKFNEKDGHVERKSKNG
          YPGSKVERS.VP.EKV.WL.EW.....PVEYTA.S.L.GP.WADPQ..E.NFSPKFNEKDGHVER....G
Retrocopy YPGSKVERSLVPHEKVSWLAEWRE<VTPVEYTASSILPGPLWADPQVGERNFSPKFNEKDGHVERRNQHG

Parental  LYEIEKWKDRDPAGRTGLVGRGLLGRWGPNHAADPIITRWKRDSSGNRIMHPVSGKHILQFVAIKRKDCG
          LYEIEK...R.PA.RTGLVG.G.LG.WGP.HA.DPI.TRWKRDS.GN.I..P.SGK.ILQFVAI.RKD.G
Retrocopy LYEIEKGRLRNPASRTGLVGQGPLGCWGPSHAVDPILTRWKRDSRGNEITPPISGKNILQFVAI*RKDHG

Parental  EWAIPGGMVDPGEKISATLKREFGEEALNSLQKTSAEKREIEEKLHKLFSQDHLVIYKGYVDDPRNTDNA
          E.AIPGGMVDPGEKISATLKR.F.EEA.NSLQK...E..E.E..LHKL.SQ.H.V.YKGYVDD.RNTDN.
Retrocopy E*AIPGGMVDPGEKISATLKR*FDEEAMNSLQKSRKEMQELERQLHKLLSQEHFVVYKGYVDDSRNTDNC

Parental  WLETEAVNYHDETGEIMDNLTLEAGDDAGKVKWVDINDKLKLYANHSQFIQLVTEKRDAHWSEDSEADC
          W..TEAVNYHDE...IMD.L.LEAG.DA.KVKWVDINDKL.LYA.HSQFIQLV.EKRDAH.SED...DC
Retrocopy WIKTEAVNYHDE---IMDHLPLEAGNDAKKVKWVDINDKLELYASHSQFIQLVAEKRDAH*SEDMYPDC

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	0.66 RPM	29.97 RPM
SRP007412_cerebellum	0.49 RPM	20.06 RPM
SRP007412_heart	0.33 RPM	11.56 RPM
SRP007412_kidney	0.43 RPM	25.62 RPM
SRP007412_liver	0.21 RPM	13.07 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_613 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_613 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_613 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_709
Pan troglodytes	retro_ptro_506
Gorilla gorilla	retro_ggor_602
Callithrix jacchus	retro_cjac_1047
Oryctolagus cuniculus	retro_ocun_990
Bos taurus	retro_btau_1112
Sus scrofa	retro_sscr_447
Canis familiaris	retro_cfam_1271
Equus caballus	retro_ecab_123

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003244	1 retrocopy	retro_amel_612,
Bos taurus	ENSBTAG00000011354	1 retrocopy	retro_btau_1112,
Canis familiaris	ENSCAFG00000009529	1 retrocopy	retro_cfam_1271,
Callithrix jacchus	ENSCJAG00000006159	1 retrocopy	retro_cjac_1047,
Equus caballus	ENSECAG00000019556	1 retrocopy	retro_ecab_123,
Echinops telfairi	ENSETEG00000019164	1 retrocopy	retro_etel_348,
Felis catus	ENSFCAG00000003315	1 retrocopy	retro_fcat_1509,
Homo sapiens	ENSG00000170502	1 retrocopy	retro_hsap_709,
Gorilla gorilla	ENSGGOG00000014777	1 retrocopy	retro_ggor_602,
Loxodonta africana	ENSLAFG00000011391	1 retrocopy	retro_lafr_224,
Macropus eugenii	ENSMEUG00000012123	4 retrocopies	retro_meug_1072, retro_meug_1345, retro_meug_1758, retro_meug_2162,
Monodelphis domestica	ENSMODG00000020738	2 retrocopies	retro_mdom_157, retro_mdom_706,
Mustela putorius furo	ENSMPUG00000002258	1 retrocopy	retro_mputfur_585,
Nomascus leucogenys	ENSNLEG00000009520	1 retrocopy	retro_nleu_464,
Oryctolagus cuniculus	ENSOCUG00000002670	2 retrocopies	retro_ocun_1045, retro_ocun_990,
Ochotona princeps	ENSOPRG00000004055	1 retrocopy	retro_opri_1152,
Pongo abelii	ENSPPYG00000014914	1 retrocopy	retro_pabe_613 ,
Pan troglodytes	ENSPTRG00000016259	1 retrocopy	retro_ptro_506,
Pteropus vampyrus	ENSPVAG00000004829	1 retrocopy	retro_pvam_475,
Sus scrofa	ENSSSCG00000009223	1 retrocopy	retro_sscr_447,
Tursiops truncatus	ENSTTRG00000004207	1 retrocopy	retro_ttru_1549,
Vicugna pacos	ENSVPAG00000004012	1 retrocopy	retro_vpac_125,