RetrogeneDB ID: retro_cjac_2949

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:136814142..136814681(+)
• Located in intron of: ENSCJAG00000003430

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000003311
• Aliases: None
• Description: None

Sequence

>retro_cjac_2949
ATGAGAATTCTCTTTACCAGAATATGGAGACTGTTCAATCACCAGGAGCACAGAGTTAGCACTGTTGGGCGGGATAATAC
AGGGAAAACTACCATCTTTTGCCAGTTTTCCATGAATGAAGTTGTACGTACATCTCCTACAACAGGAACTAATTAATGGA
GAAGACATAGTGATTAATAATACACGTTTCCTAATGTGGGATACTGGTGGCAAGAATCTCTTCGTTCTTCCTAGAACATT
TATTATACTAACACAGAGTTTGTAATAGTTGTTGTGGACAGTACAGACAGAGAGAGGATTTCTTTAACTAGAGAAGAACT
TATAAAATGTTAGCACATGAGGACCTAAGAAAAGCTGGATTGCTGATTTTTGCTAATAAACAAGGTGTTAAAGAATGCAT
GACAGTAGCAGAAATCTCCCAGTTTTTGAAGCTAACTTCTATTAAAGATCATCAGTGGCATATCCAGGCATGCTGTGCTC
TAACTGGAGAGGGATTGTGCCAAGGACTTGAATGGATGATGTCGTGACTTAAGACTAGA

Alignment

ORF - retro_cjac_2949 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGILFTRIWRLFNHQEHKVIIVGLDNA-GKTTILYQFS-MNEVVHTSPTIGSNVEEIVINNTRFLMWDIG
          M.ILFTRIWRLFNHQEH.V..VG.DN..GK......F..M...VH.......N.E.IVINNTRFLMWD.G
Retrocopy MRILFTRIWRLFNHQEHRVSTVGRDNT>GKLPSFASFP*MKLYVHLLQQELINGEDIVINNTRFLMWDTG

Parental  G-QESLRSSWNTYYTNTEFVIVVVDSTDRERISVTREEL-YKMLAHEDLRKAGLLIFANKQDVKECMTVA
          G.QESLRSS.N.YYTNTEFVIVVVDSTDRERIS.TREEL.YKMLAHEDLRKAGLLIFANKQ.VKECMTVA
Retrocopy G<QESLRSS*NIYYTNTEFVIVVVDSTDRERISLTREEL<YKMLAHEDLRKAGLLIFANKQGVKECMTVA

Parental  EISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRLKIR
          EISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMS.LK.R
Retrocopy EISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMS*LKTR

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	0.55 RPM	33.99 RPM
SRP051959_heart	0.18 RPM	52.02 RPM
SRP051959_kidney	0.29 RPM	37.78 RPM
SRP051959_liver	0.09 RPM	29.33 RPM
SRP051959_lung	0.49 RPM	52.66 RPM
SRP051959_lymph_node	0.25 RPM	33.06 RPM
SRP051959_skeletal_muscle	0.20 RPM	35.25 RPM
SRP051959_spleen	0.53 RPM	44.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2949 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2949 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2949 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 118 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005062	25 retrocopies	retro_chof_1109, retro_chof_1132, retro_chof_1205, retro_chof_1218, retro_chof_1407, retro_chof_1414, retro_chof_1443, retro_chof_1573, retro_chof_1712, retro_chof_1953, retro_chof_206, retro_chof_2081, retro_chof_2131, retro_chof_2142, retro_chof_2433, retro_chof_2464, retro_chof_2470, retro_chof_2713, retro_chof_373, retro_chof_547, retro_chof_836, retro_chof_857, retro_chof_865, retro_chof_972, retro_chof_98,
Callithrix jacchus	ENSCJAG00000001966	1 retrocopy	retro_cjac_2938,
Callithrix jacchus	ENSCJAG00000003311	9 retrocopies	retro_cjac_1054, retro_cjac_1111, retro_cjac_1255, retro_cjac_1921, retro_cjac_2949 , retro_cjac_3920, retro_cjac_4131, retro_cjac_4175, retro_cjac_4211,
Cavia porcellus	ENSCPOG00000005209	1 retrocopy	retro_cpor_913,
Dasypus novemcinctus	ENSDNOG00000013331	16 retrocopies	retro_dnov_105, retro_dnov_1165, retro_dnov_1244, retro_dnov_1953, retro_dnov_2159, retro_dnov_226, retro_dnov_2265, retro_dnov_2268, retro_dnov_2344, retro_dnov_2394, retro_dnov_563, retro_dnov_671, retro_dnov_713, retro_dnov_811, retro_dnov_818, retro_dnov_881,
Equus caballus	ENSECAG00000023672	1 retrocopy	retro_ecab_1087,
Erinaceus europaeus	ENSEEUG00000009350	3 retrocopies	retro_eeur_240, retro_eeur_642, retro_eeur_699,
Felis catus	ENSFCAG00000014742	2 retrocopies	retro_fcat_569, retro_fcat_65,
Homo sapiens	ENSG00000162980	5 retrocopies	retro_hsap_2549, retro_hsap_4715, retro_hsap_4768, retro_hsap_4894, retro_hsap_721,
Gorilla gorilla	ENSGGOG00000002066	5 retrocopies	retro_ggor_1131, retro_ggor_1594, retro_ggor_2930, retro_ggor_2971, retro_ggor_3056,
Loxodonta africana	ENSLAFG00000032104	4 retrocopies	retro_lafr_1178, retro_lafr_1228, retro_lafr_1244, retro_lafr_599,
Microcebus murinus	ENSMICG00000015788	7 retrocopies	retro_mmur_1271, retro_mmur_1487, retro_mmur_1586, retro_mmur_1618, retro_mmur_468, retro_mmur_652, retro_mmur_923,
Macaca mulatta	ENSMMUG00000010521	5 retrocopies	retro_mmul_2519, retro_mmul_2543, retro_mmul_2630, retro_mmul_616, retro_mmul_641,
Monodelphis domestica	ENSMODG00000003978	1 retrocopy	retro_mdom_75,
Mustela putorius furo	ENSMPUG00000000396	2 retrocopies	retro_mputfur_1477, retro_mputfur_352,
Mus musculus	ENSMUSG00000036093	1 retrocopy	retro_mmus_2232,
Nomascus leucogenys	ENSNLEG00000011191	2 retrocopies	retro_nleu_1259, retro_nleu_2280,
Otolemur garnettii	ENSOGAG00000011424	6 retrocopies	retro_ogar_1879, retro_ogar_2112, retro_ogar_2675, retro_ogar_3146, retro_ogar_3465, retro_ogar_728,
Pongo abelii	ENSPPYG00000012848	4 retrocopies	retro_pabe_3711, retro_pabe_3806, retro_pabe_3832, retro_pabe_621,
Pan troglodytes	ENSPTRG00000012538	5 retrocopies	retro_ptro_1486, retro_ptro_3134, retro_ptro_3175, retro_ptro_3262, retro_ptro_514,
Ictidomys tridecemlineatus	ENSSTOG00000016326	1 retrocopy	retro_itri_62,
Tupaia belangeri	ENSTBEG00000011511	8 retrocopies	retro_tbel_1173, retro_tbel_1540, retro_tbel_3202, retro_tbel_3464, retro_tbel_3681, retro_tbel_3835, retro_tbel_4207, retro_tbel_4665,
Tursiops truncatus	ENSTTRG00000015564	2 retrocopies	retro_ttru_1008, retro_ttru_1843,
Vicugna pacos	ENSVPAG00000002172	2 retrocopies	retro_vpac_318, retro_vpac_399,