RetrogeneDB ID: retro_cjac_398

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:59349430..59350021(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000034899
• Aliases: None
• Description: None

Sequence

>retro_cjac_398
GACAAAGTCATATGGAAGCATCTCCTCATTGATGGAGATAGTGCTGGAGATGATTGGAGAATTAATCTGCTAGTGAAGAG
TTTCATTAAATGGTGCAACTCTGGGTCCCAGGAAGAAGGATATAGCCAGTACCAGCGTATGCTGAGCACACTGTCTCAAT
GTGAATTTTCAATGGGCAAAACTTTACGAGTATATGATATGAATCTCAGAGAAATGGAAAATTACGAAAAAATTTACAAG
GAAATAGAATGTAGCATTGCTGGAACACATTAAAAAATTGCTGAGTGCAAAAAGCAAATTCTTCGCGCAAAATGAATACG
AAAAAATCGCCAAGAATATGATGCTTTGGCAAAAGTGATCCAGCATCATCCAGACAGGCATGAGACATTAAAGGAACTAG
AAGCTCTGGGAAAAGAATTAGAGCATCTTTCACATATTAAAAAAAGTGTCGAAAAGCTGGAATTGAGACAGAAACAGGTT
CACATTCTTCTTAGAACCATCCATGAACTTCAGCAAACATTGGAAAATGATGAAAAACTCTCAGAGGTAGAAGAAGCTCA
GGACGCAAGCATGGAAACAGATCCTGAGCCA

Alignment

ORF - retro_cjac_398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.41 %
• Parental protein coverage: 97.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEVIRKRLLIDGDGAGDDRRINLLVKSFIKWCNSGSQEEGYSQYQRMLSTLSQCEFSMGKTLLVYDMNLR
          D.VI.K.LLIDGD.AGDD.RINLLVKSFIKWCNSGSQEEGYSQYQRMLSTLSQCEFSMGKTL.VYDMNLR
Retrocopy DKVIWKHLLIDGDSAGDDWRINLLVKSFIKWCNSGSQEEGYSQYQRMLSTLSQCEFSMGKTLRVYDMNLR

Parental  EMENYEKIYKEIECSIAGAHEKIAECKKQILQAKRIRKNRQEYDALAKVIQHHPDRHETLKELEALGKEL
          EMENYEKIYKEIECSIAG.H.KIAECKKQIL.AK.IRKNRQEYDALAKVIQHHPDRHETLKELEALGKEL
Retrocopy EMENYEKIYKEIECSIAGTH*KIAECKKQILRAK*IRKNRQEYDALAKVIQHHPDRHETLKELEALGKEL

Parental  EHLSHIKESVEDKLELRRKQFHVLLSTIHELQQTLENDEKLSEVEEAQDASMETDPKP
          EHLSHIK.SVE.KLELR.KQ.H.LL.TIHELQQTLENDEKLSEVEEAQDASMETDP.P
Retrocopy EHLSHIKKSVE-KLELRQKQVHILLRTIHELQQTLENDEKLSEVEEAQDASMETDPEP

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	6.19 RPM
SRP051959_heart	0.00 RPM	7.72 RPM
SRP051959_kidney	0.00 RPM	8.52 RPM
SRP051959_liver	0.00 RPM	9.99 RPM
SRP051959_lung	0.00 RPM	6.67 RPM
SRP051959_lymph_node	0.00 RPM	6.37 RPM
SRP051959_skeletal_muscle	0.02 RPM	17.60 RPM
SRP051959_spleen	0.00 RPM	5.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_398 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_398 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_398 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012170	2 retrocopies	retro_chof_2655, retro_chof_722,
Callithrix jacchus	ENSCJAG00000034899	2 retrocopies	retro_cjac_354, retro_cjac_398 ,
Cavia porcellus	ENSCPOG00000007930	2 retrocopies	retro_cpor_1127, retro_cpor_1164,
Dasypus novemcinctus	ENSDNOG00000005917	5 retrocopies	retro_dnov_2083, retro_dnov_2129, retro_dnov_2335, retro_dnov_2374, retro_dnov_380,
Equus caballus	ENSECAG00000000497	1 retrocopy	retro_ecab_1097,
Echinops telfairi	ENSETEG00000015076	3 retrocopies	retro_etel_1093, retro_etel_1858, retro_etel_85,
Loxodonta africana	ENSLAFG00000001987	2 retrocopies	retro_lafr_585, retro_lafr_774,
Macropus eugenii	ENSMEUG00000006342	4 retrocopies	retro_meug_1481, retro_meug_1524, retro_meug_1599, retro_meug_1861,
Myotis lucifugus	ENSMLUG00000012060	1 retrocopy	retro_mluc_369,
Monodelphis domestica	ENSMODG00000003009	1 retrocopy	retro_mdom_315,
Oryctolagus cuniculus	ENSOCUG00000021860	1 retrocopy	retro_ocun_124,
Otolemur garnettii	ENSOGAG00000024865	1 retrocopy	retro_ogar_2733,
Ochotona princeps	ENSOPRG00000016403	2 retrocopies	retro_opri_1031, retro_opri_345,
Sorex araneus	ENSSARG00000013894	1 retrocopy	retro_sara_41,
Sarcophilus harrisii	ENSSHAG00000011615	1 retrocopy	retro_shar_240,
Sus scrofa	ENSSSCG00000011491	1 retrocopy	retro_sscr_1182,
Ictidomys tridecemlineatus	ENSSTOG00000012552	1 retrocopy	retro_itri_1425,
Tupaia belangeri	ENSTBEG00000007069	1 retrocopy	retro_tbel_49,
Tursiops truncatus	ENSTTRG00000013618	3 retrocopies	retro_ttru_1365, retro_ttru_23, retro_ttru_957,
Vicugna pacos	ENSVPAG00000010083	1 retrocopy	retro_vpac_68,