RetrogeneDB ID: retro_cjac_3229

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:74444998..74445413(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000015613
• Aliases: None
• Description: None

Sequence

>retro_cjac_3229
CTGGCCTCAGCTCTCCCCTACTGTATCATAGAAGCAGTCACCTGGGTAGGCCCTCCAGACTTCCTGCACCCCACCCTAAG
TCCCTTGTGCACTTCAGGTCACTGCAATTCCCTTGGGTCACATGAAATAAATGAGGAGTTTGATGCTTGCTGGGTGACAT
ACTACAACAAGCCAGATATAGACGCCTGGGAATTGCATAAAGAAAATAACACATTTATTAGCTATGATCTGGTTGAGAGC
CCAAAATTATTAATGCTGCTTATAGGCAACTAAATGCTTTGGCTACTGAAGTTCTCATCCTAGGGACTGCTAAAGACAAA
GCAGCACCTGATAAGGAAATCTACCCCTATGTCATCCAGAACTAATACAAATTTTAAATGTATTGGGCATATCCACTCCA
GAGGAACTGGACTTG

Alignment

ORF - retro_cjac_3229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.11 %
• Parental protein coverage: 97.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LGAALRRCAVAATARAGPRGLLHSAPTPGPAAAIQSVRCYSHGSSETDEEFDARWVTYFNKPDIDAWELR
          L..AL..C...A....GP...LH..PT..P.....S..C.S.GS.E..EEFDA.WVTY.NKPDIDAWEL.
Retrocopy LASALPYCIIEAVTWVGPPDFLH--PTLSPLCT--SGHCNSLGSHEINEEFDACWVTYYNKPDIDAWELH

Parental  KGINTLVTYDLVP-EPKIIDAALRACRRLNDFASTVRILEAVKDKAGPHKEIYPYVIQ-ELRPTLNELGI
          K..NT...YDLV..EPKII.AA.R....LN..A..V.IL...KDKA.P.KEIYPYVIQ.EL...LN.LGI
Retrocopy KENNTFISYDLVE<EPKIINAAYR---QLNALATEVLILGTAKDKAAPDKEIYPYVIQ<ELIQILNVLGI

Parental  STPEELGL
          STPEEL.L
Retrocopy STPEELDL

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	19.79 RPM
SRP051959_heart	0.00 RPM	56.46 RPM
SRP051959_kidney	0.00 RPM	22.30 RPM
SRP051959_liver	0.00 RPM	22.29 RPM
SRP051959_lung	0.00 RPM	7.19 RPM
SRP051959_lymph_node	0.00 RPM	8.54 RPM
SRP051959_skeletal_muscle	0.00 RPM	94.89 RPM
SRP051959_spleen	0.00 RPM	8.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3229 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3229 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3229 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1036
Pan troglodytes	retro_ptro_706
Gorilla gorilla	retro_ggor_817

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008643	2 retrocopies	retro_amel_546, retro_amel_706,
Bos taurus	ENSBTAG00000017267	1 retrocopy	retro_btau_711,
Canis familiaris	ENSCAFG00000017977	1 retrocopy	retro_cfam_29,
Choloepus hoffmanni	ENSCHOG00000006108	4 retrocopies	retro_chof_1291, retro_chof_1434, retro_chof_2330, retro_chof_695,
Callithrix jacchus	ENSCJAG00000015613	6 retrocopies	retro_cjac_2567, retro_cjac_3167, retro_cjac_3229 , retro_cjac_703, retro_cjac_9, retro_cjac_982,
Cavia porcellus	ENSCPOG00000024832	3 retrocopies	retro_cpor_1248, retro_cpor_770, retro_cpor_970,
Felis catus	ENSFCAG00000010587	3 retrocopies	retro_fcat_1100, retro_fcat_1201, retro_fcat_253,
Homo sapiens	ENSG00000178741	3 retrocopies	retro_hsap_1036, retro_hsap_1337, retro_hsap_1416,
Gorilla gorilla	ENSGGOG00000024426	3 retrocopies	retro_ggor_1041, retro_ggor_1096, retro_ggor_817,
Loxodonta africana	ENSLAFG00000006266	1 retrocopy	retro_lafr_1192,
Macropus eugenii	ENSMEUG00000013942	2 retrocopies	retro_meug_1280, retro_meug_784,
Myotis lucifugus	ENSMLUG00000013702	1 retrocopy	retro_mluc_337,
Macaca mulatta	ENSMMUG00000011677	2 retrocopies	retro_mmul_2176, retro_mmul_2255,
Monodelphis domestica	ENSMODG00000028168	1 retrocopy	retro_mdom_830,
Mustela putorius furo	ENSMPUG00000017314	1 retrocopy	retro_mputfur_652,
Mus musculus	ENSMUSG00000000088	2 retrocopies	retro_mmus_1413, retro_mmus_742,
Nomascus leucogenys	ENSNLEG00000014708	4 retrocopies	retro_nleu_1821, retro_nleu_1838, retro_nleu_2647, retro_nleu_909,
Otolemur garnettii	ENSOGAG00000005611	5 retrocopies	retro_ogar_1540, retro_ogar_2150, retro_ogar_2432, retro_ogar_2585, retro_ogar_604,
Pongo abelii	ENSPPYG00000006652	1 retrocopy	retro_pabe_197,
Pan troglodytes	ENSPTRG00000007289	3 retrocopies	retro_ptro_706, retro_ptro_914, retro_ptro_969,
Pteropus vampyrus	ENSPVAG00000012957	1 retrocopy	retro_pvam_438,
Rattus norvegicus	ENSRNOG00000018816	1 retrocopy	retro_rnor_1867,
Sarcophilus harrisii	ENSSHAG00000015941	2 retrocopies	retro_shar_238, retro_shar_422,
Tursiops truncatus	ENSTTRG00000008004	2 retrocopies	retro_ttru_161, retro_ttru_765,