RetrogeneDB ID: retro_cjac_1617

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:72540739..72541250(-)
• Located in intron of: ENSCJAG00000017993

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPMT
• Ensembl ID: ENSCJAG00000006906
• Aliases: None
• Description: thiopurine S-methyltransferase [Source:HGNC Symbol;Acc:12014]

Sequence

>retro_cjac_1617
GTTGAGATGAAATGGGTTCCAGACCAGGGACATAGTGTCGTCGGTGCATAAATCAGTGAACTTGGGATACAAGAATTTTT
TACAGAGCAGAATCTTTCTTACCCAGAAGAACTAATCACCTAAGTTCCTGGAGCCAAAGTATGTAAGAGTTCTTCACAGA
ACATTTCATTCACTGTTGCAGCATTTTTGATCTTCCTCGAACACATATCAACAAATTTGACAGAATTGGGGATAGGGGAG
CGCTGGCTGCAGGAATCCAGGAGGTTTCAAACTTATGCAGATACAGTACTGTCCGTCCCGGGCAAAGGGCTTCAGTGCCT
CGTGTGTGTTCTTCCTTATGACCCAACCAAACACCGGGCCCACCGGCTTATGTTCCACGTGCTGAAATCGGATGGCTGTT
CAGTACGGTGTGTGATATTCATCGTCTTGAGAAGACTGATGCTTCTGAAGAACGCTGAGAAAGTTGAGGAACCGACTACA
TTTGGAAAAGTTGTATCTACTTACAGAAAAG

Alignment

ORF - retro_cjac_1617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.23 %
• Parental protein coverage: 70.2 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VEMKWFADRGHSVIGVEISELAIREFFTEQNLSYSEEPITEIPGAKVFKSSSGNIS-LYCCSIFDLPRTN
          VEMKW..D.GHSV.G..ISEL.I.EFFTEQNLSY.EE.IT..PGAKV.KSSS.NIS...CCSIFDLPRT.
Retrocopy VEMKWVPDQGHSVVGA*ISELGIQEFFTEQNLSYPEELIT*VPGAKVCKSSSQNIS<IHCCSIFDLPRTH

Parental  IGKFDRIWDRGALVA-INPGDRK-CYAEIMSFLLGKKFQYLMCVLSYDPTKH-PGPPFYVPQAEIERLFG
          I.KFDRI.DRGAL.A..NPG..K..YA.......GK..Q.L.CVL.YDPTKH.PGPP.YVP.AEI..LF.
Retrocopy INKFDRIGDRGALAA<RNPGGFK<TYADTVLSVPGKGLQCLVCVLPYDPTKH<PGPPAYVPRAEIGWLFS

Parental  KICNIHCLEKVDAFEERHRSWGIDYLF-EKLYLLTEK
          ..C.IH.LEK.DA.EER..S.G.DY...EKLYLLTEK
Retrocopy TVCDIHRLEKTDASEER*ES*GTDYIW<EKLYLLTEK

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	1.91 RPM	1.75 RPM
SRP051959_heart	1.47 RPM	2.05 RPM
SRP051959_kidney	0.62 RPM	6.39 RPM
SRP051959_liver	0.63 RPM	2.71 RPM
SRP051959_lung	1.12 RPM	1.64 RPM
SRP051959_lymph_node	0.53 RPM	1.80 RPM
SRP051959_skeletal_muscle	0.68 RPM	1.00 RPM
SRP051959_spleen	0.61 RPM	2.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1617 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1617 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1617 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008676	27 retrocopies	retro_chof_1029, retro_chof_1047, retro_chof_1184, retro_chof_1209, retro_chof_1425, retro_chof_1451, retro_chof_1483, retro_chof_1498, retro_chof_168, retro_chof_1830, retro_chof_1946, retro_chof_195, retro_chof_2039, retro_chof_2203, retro_chof_2543, retro_chof_2562, retro_chof_2649, retro_chof_330, retro_chof_503, retro_chof_626, retro_chof_637, retro_chof_684, retro_chof_743, retro_chof_761, retro_chof_78, retro_chof_79, retro_chof_921,
Callithrix jacchus	ENSCJAG00000006906	2 retrocopies	retro_cjac_1617 , retro_cjac_4192,
Cavia porcellus	ENSCPOG00000005295	1 retrocopy	retro_cpor_666,
Dasypus novemcinctus	ENSDNOG00000004842	1 retrocopy	retro_dnov_965,
Homo sapiens	ENSG00000137364	4 retrocopies	retro_hsap_1884, retro_hsap_2781, retro_hsap_4835, retro_hsap_4868,
Gorilla gorilla	ENSGGOG00000016155	4 retrocopies	retro_ggor_1381, retro_ggor_1938, retro_ggor_3014, retro_ggor_3041,
Loxodonta africana	ENSLAFG00000011632	1 retrocopy	retro_lafr_438,
Macaca mulatta	ENSMMUG00000016627	3 retrocopies	retro_mmul_1445, retro_mmul_2576, retro_mmul_2609,
Mus musculus	ENSMUSG00000021376	1 retrocopy	retro_mmus_2738,
Nomascus leucogenys	ENSNLEG00000001548	4 retrocopies	retro_nleu_1806, retro_nleu_2001, retro_nleu_2710, retro_nleu_682,
Oryctolagus cuniculus	ENSOCUG00000003854	2 retrocopies	retro_ocun_1255, retro_ocun_1370,
Otolemur garnettii	ENSOGAG00000007738	2 retrocopies	retro_ogar_1972, retro_ogar_701,
Pongo abelii	ENSPPYG00000016263	4 retrocopies	retro_pabe_1563, retro_pabe_2235, retro_pabe_3758, retro_pabe_3786,
Pan troglodytes	ENSPTRG00000017756	5 retrocopies	retro_ptro_1265, retro_ptro_1882, retro_ptro_3217, retro_ptro_3218, retro_ptro_3243,