RetrogeneDB ID: retro_cjac_1343

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:54157908..54158348(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HINT2
• Ensembl ID: ENSCJAG00000010068
• Aliases: None
• Description: histidine triad nucleotide binding protein 2 [Source:HGNC Symbol;Acc:18344]

Sequence

>retro_cjac_1343
GCCCTGCGCAGAGCCATGGCGGCCATGGGGTGGCGCAGTGCACACATCTGAGGAGCTGGAGGTGTGACTGGTGGGAATGA
AACAAGCAAGGGCCAGCTGGCAACTTGTAAGGGTGTAGCCCCAACCATCTTCTATAGGATACTGGACCATAGCCTCCCAG
CCTACATTCTGTATGAGGACTAGCAGTGTCTTCTGTTCCCTGATGTGGCTCCTTAGGCTCCTATGAACTTTCTGGTCATT
CCTAAGAAGCCCATTCCTCATATTAACCAGGCTGAAGAAGAAAGCAGCTCCTAGCACATCTACTCCTTATGTCTAAGAAG
TAGGCTGAGGGCCTGGGAGATGGATACTGACTTGTGATCAATGATGAGAAGCTGAGTGCACAATCTGTAAATTACCTGCA
TGTTTACTTACTTGGGAGCTGACAGCTTTGGTGGCCTCCA

Alignment

ORF - retro_cjac_1343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.58 %
• Parental protein coverage: 92.02 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AARRAVAAARVRGAQVRGAAGVTDGNEVTKAQQATPGGAAPTIFSRILDRSLPADILYEDQQCLVFRDVA
          A.RRA.AA...R.A...GA.GVT.GNE..K.Q.AT..G.APTIF.RILD.SLPA.ILYED.QCL.F.DVA
Retrocopy ALRRAMAAMGWRSAHI*GAGGVTGGNETSKGQLATCKGVAPTIFYRILDHSLPAYILYED*QCLLFPDVA

Parental  PQAPVHFLVIPKKPIPRISQAEEED-QQLLGHLLIVAKKIAKAEGLGDGYRLVINDGKLGAQSVYHLHIH
          P.AP..FLVIPKKPIP.I.QAEEE..Q.L...LL...KK.A...G..DGY.LVIND.KL.AQSV..LH..
Retrocopy P*APMNFLVIPKKPIPHINQAEEES<QLLAHLLL-MSKK*AEGLG--DGY*LVINDEKLSAQSVNYLHVY

Parental  VLGGRQLQWPP
          .LG..QL.WPP
Retrocopy LLGS*QLWWPP

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	0.02 RPM	4.66 RPM
SRP051959_heart	0.09 RPM	5.49 RPM
SRP051959_kidney	0.02 RPM	8.70 RPM
SRP051959_liver	0.00 RPM	7.28 RPM
SRP051959_lung	0.05 RPM	2.44 RPM
SRP051959_lymph_node	0.05 RPM	2.37 RPM
SRP051959_skeletal_muscle	0.02 RPM	9.46 RPM
SRP051959_spleen	0.00 RPM	2.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1343 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1343 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1343 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2603
Pan troglodytes	retro_ptro_1754
Gorilla gorilla	retro_ggor_1823
Pongo abelii	retro_pabe_2310
Macaca mulatta	retro_mmul_1509

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011444	1 retrocopy	retro_btau_1129,
Callithrix jacchus	ENSCJAG00000010068	1 retrocopy	retro_cjac_1343 ,
Callithrix jacchus	ENSCJAG00000014398	3 retrocopies	retro_cjac_134, retro_cjac_142, retro_cjac_87,
Cavia porcellus	ENSCPOG00000000419	1 retrocopy	retro_cpor_181,
Dasypus novemcinctus	ENSDNOG00000009083	2 retrocopies	retro_dnov_201, retro_dnov_854,
Echinops telfairi	ENSETEG00000017929	1 retrocopy	retro_etel_486,
Homo sapiens	ENSG00000137133	1 retrocopy	retro_hsap_2603,
Gorilla gorilla	ENSGGOG00000011265	1 retrocopy	retro_ggor_1823,
Loxodonta africana	ENSLAFG00000015022	1 retrocopy	retro_lafr_737,
Macaca mulatta	ENSMMUG00000016337	1 retrocopy	retro_mmul_1509,
Nomascus leucogenys	ENSNLEG00000026914	1 retrocopy	retro_nleu_1534,
Oryctolagus cuniculus	ENSOCUG00000027206	1 retrocopy	retro_ocun_66,
Otolemur garnettii	ENSOGAG00000011830	1 retrocopy	retro_ogar_765,
Pongo abelii	ENSPPYG00000019082	1 retrocopy	retro_pabe_2310,
Pan troglodytes	ENSPTRG00000020923	1 retrocopy	retro_ptro_1754,
Pteropus vampyrus	ENSPVAG00000003028	1 retrocopy	retro_pvam_842,
Tupaia belangeri	ENSTBEG00000013020	1 retrocopy	retro_tbel_4676,
Tarsius syrichta	ENSTSYG00000002700	7 retrocopies	retro_tsyr_1210, retro_tsyr_1356, retro_tsyr_1483, retro_tsyr_1485, retro_tsyr_311, retro_tsyr_468, retro_tsyr_48,
Tursiops truncatus	ENSTTRG00000011932	1 retrocopy	retro_ttru_1302,