RetrogeneDB ID: retro_cjac_1047

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:77996836..77997602(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT9
• Ensembl ID: ENSCJAG00000006159
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 9 [Source:HGNC Symbol;Acc:8056]

Sequence

>retro_cjac_1047
GCTGGAAGCCACCTGGGCAAGGCTTTAGTGACCGTGTTTCCCTTCGTGACCTTGGCCTCTGTGATAGGCAGGCCTGGCAG
CTGCCCCAACTTCCCAGCCAGCTGGAGCCTGTTTTCCTCACGTGGGTTTCCTCTAAACTTCATCATGTCAGGTTCGAAGC
GTACTGCTGAGAAGCCCCACGAGAAGGCCTGGACATCTCCCTACCCTGGCTCCAAGGTGGAGCGAAGCTCGGTTCCGGAT
GAGAAAGTGAGCTGACTGGCCGAGTGGTGAGAGTACACGCCCGTGGAATACAATGTCATCTCTGTCTTGGCCGTGCCCGT
GTGGGCAGACCCTCAGGTGGGCGAAAGGAACTTCTCTCCTAAGTTTAACGAAAAGGATGGGCATGTGGAGAGAAGGAGCC
AGCATGGCCTGTATGAGATTGAGAAGGGTAGACCCAGAAATCCTGCAAGTTGGGCAGGATTGGTTGGCTGAGGGCTTTTG
GGCCGTTGGGGCCCCACTCATGCTGCAGATCCCATCTTAACCAGGTGGAAAAGGGATAGCAAGGGAAATGAAATTACCCA
CCCTATTTCTTGGGGGAAAATATCCTGCAATTTGTAGCCGTCAAAAGGAAGGAATGTGGAGAATGGGCAATCCCAGGGTG
GATGGTTGATCCAGGAGAGAAAATTAGTACTACTTGAAGAGAGAATTTGGTGAGGAGGTCATGAACTCTCTACAGAAATC
TAGGGGAGAAGTGCAGGTGTTGGAGAGACAATTTCACAAACTCTTC

Alignment

ORF - retro_cjac_1047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.8 %
• Parental protein coverage: 73.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGRVLGKALAAVSLSVALASVTVRSSGCRGIPTFRNSFSSCWFHLNTNIMSGSNGSKENSHNKARTSPYP
          AG..LGKAL..V...V.LASV..R...C...P.....FSS..F.LN..IMSGS....E..H.KA.TSPYP
Retrocopy AGSHLGKALVTVFPFVTLASVIGRPGSCPNFPASWSLFSSRGFPLNF-IMSGSKRTAEKPHEKAWTSPYP

Parental  GSKVQRSQVPNEKVGWVVEWQDYNPVEYTAVSVLAGPRWADPQISESNFSPKFNEKDGHVERKSQNGLYE
          GSKV.RS.VP.EKV....EW..Y.PVEY...SVLA.P.WADPQ..E.NFSPKFNEKDGHVER.SQ.GLYE
Retrocopy GSKVERSSVPDEKVS*LAEW*EYTPVEYNVISVLAVPVWADPQVGERNFSPKFNEKDGHVERRSQHGLYE

Parental  IENGRPRNPAGRTGLVGRGLLGRWGPNHAADPIITRWKRDSSGNKIIHPVS-GK-HILQFVAIKRKDCGE
          IE.GRPRNPA...GLVG.GLLGRWGP.HAADPI.TRWKRDS.GN.I.HP.S.GK..ILQFVA.KRK.CGE
Retrocopy IEKGRPRNPASWAGLVG*GLLGRWGPTHAADPILTRWKRDSKGNEITHPISWGK<NILQFVAVKRKECGE

Parental  WAIPGGMVDPGEKISAT-LKREFGEEALNTLQKTSAEKREIEEKLHKLF
          WAIPG.MVDPGEKIS.T.LKREFGEE..N.LQK...E....E...HKLF
Retrocopy WAIPGWMVDPGEKISTT<LKREFGEEVMNSLQKSRGEVQVLERQFHKLF

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
SRP051959_colon	0.00 RPM	10.89 RPM
SRP051959_heart	0.11 RPM	18.77 RPM
SRP051959_kidney	0.02 RPM	14.33 RPM
SRP051959_liver	0.02 RPM	21.81 RPM
SRP051959_lung	0.10 RPM	14.38 RPM
SRP051959_lymph_node	0.16 RPM	7.21 RPM
SRP051959_skeletal_muscle	0.04 RPM	17.93 RPM
SRP051959_spleen	0.06 RPM	8.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1047 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1047 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1047 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
Pongo abelii	retro_pabe_613
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,