RetrogeneDB ID: retro_cjac_2211

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:19864384..19865002(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT21
• Ensembl ID: ENSCJAG00000012724
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 21 [Source:HGNC Symbol;Acc:13870]

Sequence

>retro_cjac_2211
GGGGTCGCCCAGTTCGGCAACGTGTACATCCAGCAGACCAACTCCCTCACCCTGGAGCGCACATGAACCTATACCCTCTC
ACCAATTATACTTTTGGTACAATAGAACCCCTCTATGAGCAGGACAGCTCTGTTGCAGCCAGATTTCGGAGCATGAGGGA
AGAATTTGATCCAATTGGAATGAGGAGGACTGCAGAAGGGGTTCTGATTGTACACGAGCACCAGCTACCCCATGCTGCTA
CAGCTGGAAACAACTTCTTTCAGACTGCCTGGTGGTGAACTTAACCCAGGAGATGATGAAGTTGAAGGACTAAAACGCTT
CATGACAGGGATACTGGGTAGTCAGGATGGAGTTCTGCAAGACTGGGTCATTGGGAACTGGTGGAGACCAAACTTTGAGC
TTCCCCAGAATCCATATATTCCTGCAGGTATTACAAAGTCTAAGGAACATAAGACGTTGCTTTTGGTTCAGCTTCAAGAA
AAAGCCTTGTTTGCAGTCCCCCAAAATTACAGGCTGGCACCTGCACCATTGTTTGAATTGCATGACACTGCACCAGGATA
TGGACCCGTCATTTCTAGTTTCCCTCAGCTGTTGAGCAGATTCGATTTTACACGCAAT

Alignment

ORF - retro_cjac_2211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.57 %
• Parental protein coverage: 93.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GVTQFGNKYIQQTKPLTLERT-INLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVL
          GV.QFGN.YIQQT..LTLERT..NLYPLTNYTFGT.EPLYE.DSSVAARF..MREEFD.IGMRRT.EGVL
Retrocopy GVAQFGNVYIQQTNSLTLERT<MNLYPLTNYTFGTIEPLYEQDSSVAARFRSMREEFDPIGMRRTAEGVL

Parental  IVHEHRLPHVLLLQLGTTFF-KLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNF
          IVHEH.LPH......G..FF..LPGGELNPG.DEVEGLKR.MT.ILG.QDGVLQDWVI....GNWWRPNF
Retrocopy IVHEHQLPHA--ATAGNNFF>RLPGGELNPGDDEVEGLKRFMTGILGSQDGVLQDWVI----GNWWRPNF

Parental  EPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFN
          E.PQ.PYIPA.ITK.KEHK.L.LVQLQEKALFAVP.NY.L..APLFEL.D.APGYGP.ISS.PQLLSRF.
Retrocopy ELPQNPYIPAGITKSKEHKTLLLVQLQEKALFAVPQNYRLAPAPLFELHDTAPGYGPVISSFPQLLSRFD

Parental  FIYN
          F..N
Retrocopy FTRN

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	27.18 RPM
SRP051959_heart	0.00 RPM	27.99 RPM
SRP051959_kidney	0.00 RPM	31.79 RPM
SRP051959_liver	0.00 RPM	25.36 RPM
SRP051959_lung	0.00 RPM	28.81 RPM
SRP051959_lymph_node	0.00 RPM	30.09 RPM
SRP051959_skeletal_muscle	0.00 RPM	21.55 RPM
SRP051959_spleen	0.00 RPM	30.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2211 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2211 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016628	1 retrocopy	retro_amel_540,
Bos taurus	ENSBTAG00000010207	2 retrocopies	retro_btau_1655, retro_btau_937,
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211 , retro_cjac_4100,
Cavia porcellus	ENSCPOG00000003705	1 retrocopy	retro_cpor_1054,
Equus caballus	ENSECAG00000001043	1 retrocopy	retro_ecab_292,
Erinaceus europaeus	ENSEEUG00000003402	1 retrocopy	retro_eeur_35,
Echinops telfairi	ENSETEG00000013634	1 retrocopy	retro_etel_622,
Felis catus	ENSFCAG00000008669	1 retrocopy	retro_fcat_1843,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610,
Myotis lucifugus	ENSMLUG00000004968	2 retrocopies	retro_mluc_1576, retro_mluc_999,
Macaca mulatta	ENSMMUG00000019906	1 retrocopy	retro_mmul_1360,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Mus musculus	ENSMUSG00000031754	3 retrocopies	retro_mmus_1949, retro_mmus_1950, retro_mmus_2142,
Nomascus leucogenys	ENSNLEG00000001963	2 retrocopies	retro_nleu_1477, retro_nleu_2493,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Otolemur garnettii	ENSOGAG00000014888	2 retrocopies	retro_ogar_1450, retro_ogar_630,
Ochotona princeps	ENSOPRG00000006689	1 retrocopy	retro_opri_637,
Pteropus vampyrus	ENSPVAG00000014583	2 retrocopies	retro_pvam_533, retro_pvam_711,
Sorex araneus	ENSSARG00000006493	2 retrocopies	retro_sara_161, retro_sara_580,
Sarcophilus harrisii	ENSSHAG00000009651	1 retrocopy	retro_shar_469,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117, retro_sscr_185,
Tupaia belangeri	ENSTBEG00000007664	1 retrocopy	retro_tbel_4003,
Tarsius syrichta	ENSTSYG00000014602	4 retrocopies	retro_tsyr_1685, retro_tsyr_1888, retro_tsyr_790, retro_tsyr_988,
Tursiops truncatus	ENSTTRG00000013545	1 retrocopy	retro_ttru_1087,
Vicugna pacos	ENSVPAG00000003701	2 retrocopies	retro_vpac_340, retro_vpac_605,