RetrogeneDB ID: retro_cjac_1218

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:67814207..67814607(+)
• Located in intron of: ENSCJAG00000023118

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000004992
• Aliases: None
• Description: None

Sequence

>retro_cjac_1218
AGGCTTCAATGGCAAGTGTTGAAGATGCCACCCAAAGGAAAATGTGGCTCTGGAAAATTGGGGAAAGAAGAGAAGCCTCT
TAGAGCAGCAGTGCTGACACAAAGGCACAGAGTCCCAAACGTGATGGTGATGCAGTAAACAGACACATTCTAAGCCAAAA
AAGAAAAAAAAATGGCAAGCTCGTGAAGGCCATGGAAACATTAGTCTGGAATGAGATTCAATGAAGTGGTTTTACAATAT
AGTGAAACTAAGGACAGGTAAGGGGGTGAATTGGGTTAGGTGTCCAGTGGGTTCATGGGGGACCCTTTTGAGAAGCACCA
TTTGCCATGCTTGTAAGTGGATGGATAAGCCTATATTTACAGACCTCCTAGTAGACAGCATTTAATATCATCTTATTATG

Alignment

ORF - retro_cjac_1218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.43 %
• Parental protein coverage: 87.01 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RVQQQVSKMPPKGKSGSGKAGKGGA-ASGSDSAEKKAQGPKGGGNAVKVRHIL-CEKHSKIMEAMEKLK-
          R.Q.QV.KMPPKGK.GSGK.GK....AS.S.SA..KAQ.PK..G.AV..RHIL...K..K........K.
Retrocopy RLQWQVLKMPPKGKCGSGKLGKEEK<AS*SSSADTKAQSPKRDGDAVN-RHIL>AKKEKKMASS*RPWKH

Parental  -SGMRFNEVAAQYSEDKARQGGDLGWMTRGSM-VGPFQEAAFALPVSG-MDKPVFTDPPVKTKFGYHIIM
          .SGMRFNEV..QYSE.K.R.GG.LG....G.M..GPF.EA.FA..VSG.MDKP.FTD..V.....YH.IM
Retrocopy *SGMRFNEVVLQYSETKDR*GGELG*VSSGFM<GGPF*EAPFAMLVSG<MDKPIFTDLLVDS-I*YHLIM

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	1.18 RPM	1.31 RPM
SRP051959_heart	8.79 RPM	1.84 RPM
SRP051959_kidney	0.51 RPM	3.00 RPM
SRP051959_liver	0.93 RPM	2.86 RPM
SRP051959_lung	1.07 RPM	1.61 RPM
SRP051959_lymph_node	0.89 RPM	1.71 RPM
SRP051959_skeletal_muscle	0.07 RPM	1.51 RPM
SRP051959_spleen	7.94 RPM	1.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1218 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1218 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1218 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005801	1 retrocopy	retro_amel_1553,
Canis familiaris	ENSCAFG00000032230	1 retrocopy	retro_cfam_212,
Callithrix jacchus	ENSCJAG00000004992	10 retrocopies	retro_cjac_1218 , retro_cjac_1587, retro_cjac_1631, retro_cjac_1720, retro_cjac_1729, retro_cjac_1746, retro_cjac_1863, retro_cjac_2670, retro_cjac_2704, retro_cjac_2829,
Cavia porcellus	ENSCPOG00000011401	1 retrocopy	retro_cpor_631,
Dipodomys ordii	ENSDORG00000006985	2 retrocopies	retro_dord_109, retro_dord_352,
Felis catus	ENSFCAG00000012036	5 retrocopies	retro_fcat_1325, retro_fcat_1411, retro_fcat_581, retro_fcat_723, retro_fcat_769,
Homo sapiens	ENSG00000102309	3 retrocopies	retro_hsap_1562, retro_hsap_1604, retro_hsap_304,
Gorilla gorilla	ENSGGOG00000016008	4 retrocopies	retro_ggor_1187, retro_ggor_1210, retro_ggor_328, retro_ggor_338,
Loxodonta africana	ENSLAFG00000018261	1 retrocopy	retro_lafr_212,
Macropus eugenii	ENSMEUG00000003611	1 retrocopy	retro_meug_368,
Microcebus murinus	ENSMICG00000001640	4 retrocopies	retro_mmur_138, retro_mmur_294, retro_mmur_483, retro_mmur_674,
Myotis lucifugus	ENSMLUG00000012073	2 retrocopies	retro_mluc_2189, retro_mluc_923,
Mustela putorius furo	ENSMPUG00000005287	3 retrocopies	retro_mputfur_1285, retro_mputfur_417, retro_mputfur_858,
Mus musculus	ENSMUSG00000079480	8 retrocopies	retro_mmus_1656, retro_mmus_1703, retro_mmus_2205, retro_mmus_2741, retro_mmus_2921, retro_mmus_3673, retro_mmus_399, retro_mmus_821,
Nomascus leucogenys	ENSNLEG00000018119	1 retrocopy	retro_nleu_2957,
Oryctolagus cuniculus	ENSOCUG00000008715	2 retrocopies	retro_ocun_137, retro_ocun_835,
Pongo abelii	ENSPPYG00000020460	2 retrocopies	retro_pabe_146, retro_pabe_384,
Rattus norvegicus	ENSRNOG00000050051	6 retrocopies	retro_rnor_1755, retro_rnor_2368, retro_rnor_2575, retro_rnor_2576, retro_rnor_480, retro_rnor_553,
Sorex araneus	ENSSARG00000003732	2 retrocopies	retro_sara_201, retro_sara_248,