RetrogeneDB ID: retro_cjac_1476

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:67024811..67025783(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC39A1
• Ensembl ID: ENSCJAG00000010006
• Aliases: None
• Description: solute carrier family 39 (zinc transporter), member 1 [Source:HGNC Symbol;Acc:12876]

Sequence

>retro_cjac_1476
ATGGGGCTCTGGGAGAGCCCGAGCTCCTGGTGTGGCACCCAGAGGCGGTAGCTTTAGAGCCTCCAGTGCCTGTGGGGCTG
GAGGTGAAGTTGGGGTCCCTGGTGCTGCTGCTGGTGCTCACCCTTCTCGGCAGCCTGGTGCCCGTCTGTGTGCTGTGCCA
GCCAAGAGCTAACCATGAAGCCTCAGCTTCCTGCCAGAAAGCCCCAAGCCTAGTAAGCTGTTTTGTGGGGTGGCGTCTTT
TTGGCCACCTGTGTCCTTGACCTGCTGCCTGACCACCTGGCTGCTACAGGTGAGGCCCTGGCAGGCTTGCATGTGACGCT
CCGGTTCTCACTGCAAGAGTTCATCCTGGCCATGGGCTTCTCCCTCATCCTGGTGACAGAGCAGATCACATTGGCTTACA
AGCAGCAGTCAGGGCCGCCACCTCTGGAGGAAACAAGGGCTCTGCTGGGAACAGTGAATGGTGGGTCGCAGCATTGGCAT
GATGGACCAGGGATTCCACAGGCAAGTGGAGCCCCAGCAACCCCCTCAGCCTTGTGTGCCTGTGTCCTGCTCTTCTCCCT
GGCCCTCCACTCTGTGTTTGAGGGGCTGGCAGTAGGGCTTCAGTGAGACCAGACTCAGGCCACGGAGCTGTGCCTGGCTT
TGCTGCTCCACAAGGGGATCCTCGCTGTCAGTCTGTCCTTCCGGCTGCTGCAGAGCCACCTTGGGGCACAGGTGGTGGCT
GGCTGTGGGATCCTCTTCTCATGCATGACACCTCTAGGTGTTGGGCTGGGTGCAGCTCTGGGAGAGTGGGCAGGACCTCC
ACACCAGCTGGCCCAGTCTGTGCTAGAGGGCATGGCGGCTGACACTTTTCTCTATATCACCTTTCTGGAAATCCTGCCCC
AGGAGCTGGCCAGTTCTGAGCAAAGGATCCTCAAGGTCATTCTGCTCCTAGCAGACTTTGCCCTGCTCACTAACCTGCTC
TTCATCCAAATC

Alignment

ORF - retro_cjac_1476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGPW-GEPELLVWRPEAVASEPPVLVGLEVKLGALVLLLVLTLLCSLVPICVLRRPGANHEASASRQKAL
          MG.W.GEPELLVW.PEAVA.EPPV.VGLEVKLG.LVLLLVLTLL.SLVP.CVL..P.ANHEASAS.QKA.
Retrocopy MGLW<GEPELLVWHPEAVALEPPVPVGLEVKLGSLVLLLVLTLLGSLVPVCVLCQPRANHEASASCQKAP

Parental  SLVSCFAG-GVFLATCLLDLLPDYLAAIDEALAALHVTLQFPLQEFILAMGFFLVLVMEQITLAYKEQSG
          SLVSCF.G.GVFLATC.LDLLPD.LAA..EALA.LHVTL.F.LQEFILAMGF.L.LV.EQITLAYK.QSG
Retrocopy SLVSCFVG>GVFLATCVLDLLPDHLAATGEALAGLHVTLRFSLQEFILAMGFSLILVTEQITLAYKQQSG

Parental  PPPLEETRALLGTVNGGPQLWHDGPGVPQASGAPATPSALRACVLVFSLALHSVFEGLAVGLQRDRARAM
          PPPLEETRALLGTVNGG.Q.WHDGPG.PQASGAPATPSAL.ACVL.FSLALHSVFEGLAVGLQ.D...A.
Retrocopy PPPLEETRALLGTVNGGSQHWHDGPGIPQASGAPATPSALCACVLLFSLALHSVFEGLAVGLQ*DQTQAT

Parental  ELCLALLLHKGILAVSLSLRLLQSHLRAQVVAGCGILFSCMTPLGIGLGAALAESAGPLHQLAQSVLEGM
          ELCLALLLHKGILAVSLS.RLLQSHL.AQVVAGCGILFSCMTPLG.GLGAAL.E.AGP.HQLAQSVLEGM
Retrocopy ELCLALLLHKGILAVSLSFRLLQSHLGAQVVAGCGILFSCMTPLGVGLGAALGEWAGPPHQLAQSVLEGM

Parental  AAGTFLYITFLEILPQELASSEQRILKVILLLAGFALLTGLLFIQI
          AA.TFLYITFLEILPQELASSEQRILKVILLLA.FALLT.LLFIQI
Retrocopy AADTFLYITFLEILPQELASSEQRILKVILLLADFALLTNLLFIQI

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	23.14 RPM
SRP051959_heart	0.00 RPM	17.91 RPM
SRP051959_kidney	0.00 RPM	23.96 RPM
SRP051959_liver	0.00 RPM	21.53 RPM
SRP051959_lung	0.00 RPM	21.96 RPM
SRP051959_lymph_node	0.00 RPM	12.78 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.35 RPM
SRP051959_spleen	0.00 RPM	19.62 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1476 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1476 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1476 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010006	1 retrocopy	retro_cjac_1476 ,
Macropus eugenii	ENSMEUG00000006754	1 retrocopy	retro_meug_1551,
Microcebus murinus	ENSMICG00000010310	1 retrocopy	retro_mmur_162,
Myotis lucifugus	ENSMLUG00000013282	1 retrocopy	retro_mluc_2366,
Macaca mulatta	ENSMMUG00000005007	1 retrocopy	retro_mmul_28,
Mus musculus	ENSMUSG00000052310	1 retrocopy	retro_mmus_1899,
Oryctolagus cuniculus	ENSOCUG00000003045	1 retrocopy	retro_ocun_1792,