RetrogeneDB ID: retro_cjac_66

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:37878877..37879312(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022005
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EIF1AX
• Ensembl ID: ENSCJAG00000005371
• Aliases: None
• Description: None

Sequence

>retro_cjac_66
ATGCCCAAGAATAAAGGTAAAGGAGGTAAAAACAGACGTAGAGGTAAGAATGAGAATGAATCGGAAAAAAGAGAACTAGT
ATTCAAAGAAGACGGTCAAGAGTATGCTCAGGTGATCAAAATGTTGGGAAATGGACGGCTAGAAGCAATGTGTTTCGATG
GTGTAAAGAGGTTATGTCACATCAGAGGAAAATTGAGAAAAAAGGTTTGGATAAATACCTCCGACATAATATTGGTTGGT
CTCCGAGACTACCAGGATAACAAAGCGGATGTAATTTTAAAATACAATGCAGACGAAGCCAGAAGTCTGAAGGCATATGG
CGAGCTTCCAGAGCATGCTAAAGTCAATGAAACGGATACATTTGGTCCGGGAGATGATGATGAAATTCAGTTCGATGACA
TTGGAGATGATGATGAAGATATTGACGACATCTAA

Alignment

ORF - retro_cjac_66 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPKPSGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVW
          .PK..GKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVW
Retrocopy MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVW

Parental  INTSDIILVGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDTFGPGDDDEIQFDDIGDDDED
          INTSDIILVGLRDYQDNKADVILKYNADEARSLKAYGELPEHAK.NETDTFGPGDDDEIQFDDIGDDDED
Retrocopy INTSDIILVGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKVNETDTFGPGDDDEIQFDDIGDDDED

Parental  IDDV
          IDD.
Retrocopy IDDI

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	0.33 RPM	11.67 RPM
SRP051959_heart	0.40 RPM	11.26 RPM
SRP051959_kidney	0.67 RPM	13.13 RPM
SRP051959_liver	0.69 RPM	14.27 RPM
SRP051959_lung	0.36 RPM	10.74 RPM
SRP051959_lymph_node	0.23 RPM	10.43 RPM
SRP051959_skeletal_muscle	0.33 RPM	13.61 RPM
SRP051959_spleen	0.61 RPM	11.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_66 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_66 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_66 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012660	1 retrocopy	retro_acar_151,
Ailuropoda melanoleuca	ENSAMEG00000016604	1 retrocopy	retro_amel_1421,
Bos taurus	ENSBTAG00000017633	3 retrocopies	retro_btau_1293, retro_btau_293, retro_btau_381,
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66 ,
Dipodomys ordii	ENSDORG00000011536	1 retrocopy	retro_dord_484,
Equus caballus	ENSECAG00000006469	2 retrocopies	retro_ecab_464, retro_ecab_634,
Erinaceus europaeus	ENSEEUG00000007518	3 retrocopies	retro_eeur_408, retro_eeur_567, retro_eeur_686,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Gorilla gorilla	ENSGGOG00000012186	3 retrocopies	retro_ggor_1103, retro_ggor_363, retro_ggor_968,
Latimeria chalumnae	ENSLACG00000015565	1 retrocopy	retro_lcha_65,
Macaca mulatta	ENSMMUG00000000193	1 retrocopy	retro_mmul_1590,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pongo abelii	ENSPPYG00000020176	1 retrocopy	retro_pabe_1185,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Pteropus vampyrus	ENSPVAG00000003521	2 retrocopies	retro_pvam_780, retro_pvam_92,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sorex araneus	ENSSARG00000013528	1 retrocopy	retro_sara_324,
Sarcophilus harrisii	ENSSHAG00000010995	1 retrocopy	retro_shar_707,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,
Ictidomys tridecemlineatus	ENSSTOG00000026117	1 retrocopy	retro_itri_1839,
Tursiops truncatus	ENSTTRG00000002012	1 retrocopy	retro_ttru_1009,
Vicugna pacos	ENSVPAG00000009927	4 retrocopies	retro_vpac_47, retro_vpac_531, retro_vpac_550, retro_vpac_590,