RetrogeneDB ID: retro_cjac_3127

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:32716835..32717509(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000034832
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSCJAG00000006394
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide [Source:HGNC Symbol;Acc:12854]

Sequence

>retro_cjac_3127
TACAACGACATGGCCACCTGCATGAAGGCAGTGACCGAGCAGGGTGCCGAGCTGTCCAACGAGGAGCGCCACCTGCTCTC
CGTGGCCTACAAGAACGTGGTCAGGGGCCACAGGTCCACCTGGAGGGTCATCTTGAGCATCGAGCAGAAGACCAACACCT
CTGACAAGAAATTGCAGCTGATTAAGGACTATCGGGAGAAAGTGGAGTCTGAGCTGAGATCCATCTGAACCACAGTCCTG
GAGTTGGATAAATACTTAATAGCCAAGGCAACTAATCCAGAGAGTAAGGTCTTCTTTCGGAAAATGAAGGGTGATTACTT
CCAGTACCTTGCTGAAGTTGCATGTGGTGATGATCGAAAACAAACGATAGATAATTCCCAAGGAGCTTACCAAGAGGCAT
TTCATATAAGAAGGAGATGCAACCCACACACGTAATCCACCTGGGGCTTGCTCTTAACTTCTCTGTATTTTACTATGAGA
CTCTTAATAATCCAGAGCTTGCCTACACGCTGGCTAAAGCGGCTTTTGATGAGGCCATTGCTGAACTTGATACATTGAAT
GAAGACTCCTACAAAGACAACACTCTAATCATGTGGTTGCTTAGAGACAACCTAACATTTTGGACATCAGACAGTGCAGG
AGAAGAATGTGATGCAGCAGAAGGAGCTGGAAAC

Alignment

ORF - retro_cjac_3127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.89 %
• Parental protein coverage: 92.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YDDMATCMKAVTEQGAELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDTSDKKLQLIKDYREKVES
          Y.DMATCMKAVTEQGAELSNEER.LLSVAYKNVV.G.RS.WRVI.SIEQKT.TSDKKLQLIKDYREKVES
Retrocopy YNDMATCMKAVTEQGAELSNEERHLLSVAYKNVVRGHRSTWRVILSIEQKTNTSDKKLQLIKDYREKVES

Parental  ELRSICTTVLELLDKYLIANATNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKK
          ELRSI.TTVLE.LDKYLIA.ATNPESKVF..KMKGDYF.YLAEVACGDDRKQTIDNSQGAYQEAF.I...
Retrocopy ELRSI*TTVLE-LDKYLIAKATNPESKVFFRKMKGDYFQYLAEVACGDDRKQTIDNSQGAYQEAFHI-RR

Parental  EMQPTHPIRLGLALNFSVF-YYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTL
          ...P......GL.L....F.YYE.LNNPELA.TLAK.AFDEAIAELDTLNEDSYKD.TLIM.LLRDNLT.
Retrocopy RCNPHT*STWGLLLTSLYF<YYETLNNPELAYTLAKAAFDEAIAELDTLNEDSYKDNTLIMWLLRDNLTF

Parental  WTSDSAGEECDAAEGAEN
          WTSDSAGEECDAAEGA.N
Retrocopy WTSDSAGEECDAAEGAGN

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	0.02 RPM	68.23 RPM
SRP051959_heart	0.04 RPM	49.66 RPM
SRP051959_kidney	0.04 RPM	48.65 RPM
SRP051959_liver	0.02 RPM	33.66 RPM
SRP051959_lung	0.02 RPM	37.14 RPM
SRP051959_lymph_node	0.05 RPM	30.66 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.50 RPM
SRP051959_spleen	0.04 RPM	37.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3127 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3127 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3127 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002108	2 retrocopies	retro_btau_1180, retro_btau_86,
Choloepus hoffmanni	ENSCHOG00000004661	13 retrocopies	retro_chof_136, retro_chof_1427, retro_chof_1605, retro_chof_1835, retro_chof_2026, retro_chof_2115, retro_chof_2134, retro_chof_2233, retro_chof_429, retro_chof_481, retro_chof_489, retro_chof_527, retro_chof_863,
Callithrix jacchus	ENSCJAG00000006394	2 retrocopies	retro_cjac_2197, retro_cjac_3127 ,
Callithrix jacchus	ENSCJAG00000015844	5 retrocopies	retro_cjac_1769, retro_cjac_2164, retro_cjac_3000, retro_cjac_31, retro_cjac_881,
Callithrix jacchus	ENSCJAG00000017664	2 retrocopies	retro_cjac_1002, retro_cjac_2214,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Homo sapiens	ENSG00000134308	2 retrocopies	retro_hsap_3004, retro_hsap_8,
Gorilla gorilla	ENSGGOG00000001569	1 retrocopy	retro_ggor_2081,
Macropus eugenii	ENSMEUG00000014442	7 retrocopies	retro_meug_1122, retro_meug_1208, retro_meug_1259, retro_meug_1549, retro_meug_1918, retro_meug_2106, retro_meug_538,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Mustela putorius furo	ENSMPUG00000013252	2 retrocopies	retro_mputfur_1132, retro_mputfur_730,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
Pongo abelii	ENSPPYG00000012663	4 retrocopies	retro_pabe_1165, retro_pabe_2490, retro_pabe_3391, retro_pabe_3511,
Pelodiscus sinensis	ENSPSIG00000012692	1 retrocopy	retro_psin_2,
Pan troglodytes	ENSPTRG00000011641	2 retrocopies	retro_ptro_2032, retro_ptro_3,
Pteropus vampyrus	ENSPVAG00000005334	1 retrocopy	retro_pvam_983,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,
Sorex araneus	ENSSARG00000012476	4 retrocopies	retro_sara_1, retro_sara_162, retro_sara_179, retro_sara_23,