RetrogeneDB ID: retro_cjac_1348

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:68157790..68158354(+)
• Located in intron of: ENSCJAG00000017479

Retrocopy information

• Ensembl ID: ENSCJAG00000015528
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000000319
• Aliases: None
• Description: None

Sequence

>retro_cjac_1348
ATGGCTTCCAAAAGAGCTCTAGTCATCCTGGCTAAAGGAGTGGAGGAAATGGAGACCGTCATCCCTGTAGATGTCATGAG
GCGAGCTGAGATAAAGGTCACTGTTGCAGGTCTGGCTGGAAAAGACCCAGTACAGTGTAGCCGTGATGTCATGATTTGTC
CTGATGCCAGTCTTGAAGATGCAAAAAAAGAGGGACCATATAACGTGGTGGTTCTACCAGGAGGTAATCTGGGTACACAA
AATTTATCTGAGTCTGCTGCTGTGAAGGAGATACTGAAGGAACAGGAAAACTGGAAGGGCCTGACAGCCGCCATCTGTGT
AGGTCCTACTGCTCTGTTGGCTCATGAAATAGGTTTTGGAAGTAAAGTTACAACACATCCGTTTACTAAAGACAAAACGA
TGAAAGGAGGTCATTACACCTACTCTGAGAATCGGGTGGATAAGGACAGCCTGATTCTTACAAGCCGTGGGCCTGGGACC
GGCTTTGAGTTTGCGCTTGCAATTGTTGAAGCTCTGAACTGCAAGGAGGTGGCGGCTCAAGTGAAGGCTCCACTTGCTCT
TAAA

Alignment

ORF - retro_cjac_1348 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.96 %
• Parental protein coverage: 99.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVMICPDASLEDAKKEGPYDVV
          MASKRALVILAKG.EEMETVIPVDVMRRA.IKVTVAGLAGKDPVQCSRDVMICPDASLEDAKKEGPY.VV
Retrocopy MASKRALVILAKGVEEMETVIPVDVMRRAEIKVTVAGLAGKDPVQCSRDVMICPDASLEDAKKEGPYNVV

Parental  VLPGGNLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGFGSKVTTHPLAKDKMMNGGHYT
          VLPGGNLG.QNLSESAAVKEILKEQEN.KGL.AAIC.GPTALLAHEIGFGSKVTTHP..KDK.M.GGHYT
Retrocopy VLPGGNLGTQNLSESAAVKEILKEQENWKGLTAAICVGPTALLAHEIGFGSKVTTHPFTKDKTMKGGHYT

Parental  YSENRVEKDGLILTSRGPGTSFEFALAIVEALNGKEMAAQVKAPLVLK
          YSENRV.KD.LILTSRGPGT.FEFALAIVEALN.KE.AAQVKAPL.LK
Retrocopy YSENRVDKDSLILTSRGPGTGFEFALAIVEALNCKEVAAQVKAPLALK

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	0.31 RPM	21.19 RPM
SRP051959_heart	0.23 RPM	43.01 RPM
SRP051959_kidney	0.18 RPM	52.23 RPM
SRP051959_liver	0.15 RPM	49.17 RPM
SRP051959_lung	0.20 RPM	21.36 RPM
SRP051959_lymph_node	0.37 RPM	22.60 RPM
SRP051959_skeletal_muscle	0.24 RPM	107.42 RPM
SRP051959_spleen	0.40 RPM	28.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1348 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1348 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003703	1 retrocopy	retro_amel_854,
Canis familiaris	ENSCAFG00000019674	1 retrocopy	retro_cfam_1150,
Choloepus hoffmanni	ENSCHOG00000004364	7 retrocopies	retro_chof_1725, retro_chof_1877, retro_chof_2047, retro_chof_2123, retro_chof_2220, retro_chof_279, retro_chof_63,
Callithrix jacchus	ENSCJAG00000000319	4 retrocopies	retro_cjac_1348 , retro_cjac_2729, retro_cjac_3210, retro_cjac_4225,
Erinaceus europaeus	ENSEEUG00000013141	1 retrocopy	retro_eeur_233,
Echinops telfairi	ENSETEG00000010915	1 retrocopy	retro_etel_215,
Homo sapiens	ENSG00000116288	2 retrocopies	retro_hsap_4195, retro_hsap_995,
Gorilla gorilla	ENSGGOG00000012105	2 retrocopies	retro_ggor_2812, retro_ggor_795,
Microcebus murinus	ENSMICG00000008470	2 retrocopies	retro_mmur_1294, retro_mmur_690,
Nomascus leucogenys	ENSNLEG00000008790	3 retrocopies	retro_nleu_1025, retro_nleu_2320, retro_nleu_233,
Oryctolagus cuniculus	ENSOCUG00000016511	1 retrocopy	retro_ocun_1405,
Ochotona princeps	ENSOPRG00000002151	2 retrocopies	retro_opri_104, retro_opri_1173,
Pongo abelii	ENSPPYG00000001925	2 retrocopies	retro_pabe_3433, retro_pabe_840,
Pan troglodytes	ENSPTRG00000000102	3 retrocopies	retro_ptro_2848, retro_ptro_3270, retro_ptro_755,
Rattus norvegicus	ENSRNOG00000018289	2 retrocopies	retro_rnor_1229, retro_rnor_2463,
Tupaia belangeri	ENSTBEG00000009474	13 retrocopies	retro_tbel_1182, retro_tbel_1306, retro_tbel_1405, retro_tbel_1790, retro_tbel_2059, retro_tbel_220, retro_tbel_2247, retro_tbel_2551, retro_tbel_3013, retro_tbel_4047, retro_tbel_4486, retro_tbel_4538, retro_tbel_561,
Tarsius syrichta	ENSTSYG00000001455	1 retrocopy	retro_tsyr_1883,
Vicugna pacos	ENSVPAG00000011076	1 retrocopy	retro_vpac_364,