RetrogeneDB ID: retro_cjac_589

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:91816119..91816534(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3J
• Ensembl ID: ENSCJAG00000002412
• Aliases: None
• Description: None

Sequence

>retro_cjac_589
CCAGGCCCAGTGGCAGTGGTGGGGGGTTTTGACTCTCAGGGTGCTGATGAGTCCTCAGTGGGAGCCTTGGTGCAGAGGGT
AGGGGTGGCAGCACTGCTAGTGGGGACCACTGGGAAGCTGAGAATGAGGAGGTCAAAGAAAACCGGGATGATGATGATGA
CAAAAAAGAAAAAAAGGAAGCAGCAGTAAAACAAGAGATTACAATTTCAGAAAAGAAAAAAATGGCAGAGGAGATAAAAG
AGAAAGAACAACAATAGAAGAAAAGGCCAGGAGAAATGAAAAAGAGGTTAGAAGAAACTGAGAACCTAAAGTTCTAAAAC
CAGAAGAACAATTTAACAGGTAAACCACACTAAAGAAATTACAGGAAGAGTCAGACCTCAAATTAGCAAAGGAAATTTTC
ATTATTAATAATACA

Alignment

ORF - retro_cjac_589 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.47 %
• Parental protein coverage: 54.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PAPAAANGGDSDSWDADAFSVEDPVRKVG-GGGTAGGDRWEGEDEDEDVKDNWDDDDDEK-KEEAEVKPG
          P.P.A..GG..DS..AD..SV...V..VG.GG.TA.GD.WE.E.E...VK.N.DDDDD.K.K.EA.VK..
Retrocopy PGPVAVVGG-FDSQGADESSVGALVQRVG<GGSTASGDHWEAENEE--VKENRDDDDDKKEKKEAAVKQE

Parental  FSISEHIYMVQKLKRDERVFKKAIEATPVKLEEPE-EPKVLTPEEQLADKLRLKKLQEESDLELAKETFG
          ..ISE...M....K..E...KK........LEE.E.EPKVL.PEEQ......LKKLQEESDL.LAKE.F.
Retrocopy ITISEKKKMAEEIKEKEQQ*KKRPGEMKKRLEETE<EPKVLKPEEQFNR*TTLKKLQEESDLKLAKEIFI

Parental  VNNT
          .NNT
Retrocopy INNT

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	16.97 RPM
SRP051959_heart	0.02 RPM	22.96 RPM
SRP051959_kidney	0.00 RPM	21.85 RPM
SRP051959_liver	0.00 RPM	23.22 RPM
SRP051959_lung	0.00 RPM	22.66 RPM
SRP051959_lymph_node	0.00 RPM	24.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	37.52 RPM
SRP051959_spleen	0.00 RPM	23.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_589 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_589 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_589 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002412	1 retrocopy	retro_cjac_589 ,
Cavia porcellus	ENSCPOG00000012396	3 retrocopies	retro_cpor_1357, retro_cpor_1358, retro_cpor_500,
Dipodomys ordii	ENSDORG00000008339	7 retrocopies	retro_dord_208, retro_dord_364, retro_dord_451, retro_dord_470, retro_dord_633, retro_dord_738, retro_dord_746,
Equus caballus	ENSECAG00000008716	1 retrocopy	retro_ecab_635,
Echinops telfairi	ENSETEG00000005052	1 retrocopy	retro_etel_1376,
Homo sapiens	ENSG00000104131	1 retrocopy	retro_hsap_4189,
Gorilla gorilla	ENSGGOG00000000548	2 retrocopies	retro_ggor_1687, retro_ggor_41,
Macropus eugenii	ENSMEUG00000010372	1 retrocopy	retro_meug_256,
Microcebus murinus	ENSMICG00000005006	1 retrocopy	retro_mmur_100,
Monodelphis domestica	ENSMODG00000017696	1 retrocopy	retro_mdom_141,
Mus musculus	ENSMUSG00000027236	1 retrocopy	retro_mmus_18,
Nomascus leucogenys	ENSNLEG00000005568	1 retrocopy	retro_nleu_2848,
Oryctolagus cuniculus	ENSOCUG00000005376	1 retrocopy	retro_ocun_1350,
Otolemur garnettii	ENSOGAG00000004694	1 retrocopy	retro_ogar_1227,
Pongo abelii	ENSPPYG00000006431	1 retrocopy	retro_pabe_3429,