RetrogeneDB ID: retro_cjac_1790

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:52441080..52442271(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS37A
• Ensembl ID: ENSCJAG00000011769
• Aliases: None
• Description: None

Sequence

>retro_cjac_1790
ATGAGCTGGTTCTTTCCCCTGACCACCAAGAGCACCTCCTCCTCCACAGCTGGGTCCCCCGGTGGCCTCGCCAGCCTCCA
GAAGAAGAAGCAGTGCCTGATCGAGTCCTTCTGTAACTCACACTCCAGTATAGCTGAAATACAGAAAGATGTGGAATACA
GATTGCCATTCGCCATAAACAGTCTGACAATTAACATTCATATATTGCTTCCTCCATAATTTCCTCAGGAAAAACCATTG
ATCAGTGTTTATCCACCAATACGACATCACTTAATGCATAAACAAGGAGTGTATGCTACCTCTCCATTAGGGAGCAATTT
TACGATGCACTCAGATCTTGGAAAAATTATTTAGTCTGTTGAATGAGTTTTGGAAGAATCCTCCAGTTTTAGCTCCTATT
TCAACAGCATTTCCTTACCTCTACAGTAACCCAAGTGGGATGCCTTCTTATGCTTCTCGTTTTCCATTTCTTCCTCTATA
TCCCCCACAAGAAGCAAACACAAGTATCTCTTCTTTATCTGTTGCTAACACTGTTTCTTCTTCAACAACAAGTCATACCA
CAGCCAAGCCCGCCCCTCCTTCATTTGGCATCCTTTCAGATCTGCCGTTACCTGTTCCCACAATGGACATTTCAATACCA
ACAAGCCAAAATGGTTTTGGTTACAAGATGCCAGATGTCCCTGATGCATTTCCAGAACTCTCAGAACTAGGTGTGTCACA
ACCCACAGATATGAATGAATAAGAGAAGGTATTACTAGAACAGTTTCTGACTTTGCCTCAACTAAAACAAATTATTACTG
ACGAAGGTGAGTTAGTAAAAGGTATTGAGAATCTAGCAAGAAAAAAAATCTCCTTTTGGAGCCCAGCTTGGAAGCAGAAA
GACAAACTGTTTTAGGTAAGTATGAATCACTTACACAAACGGAGTCTACTTTCAGAAAGAAGAAGCAAAAGCAGCAAGAA
CTTAGTGAGAGCTGTAGTGCCAGTGCCCTCCAGGCAACGCTGAAAGTAGCTGCACCCAAAGCTAAGGGAGAACCTGATAA
TATTGCAGAAGATTTCTTGGAAGGAAAAATGGAAATAGATGGTTTTCTCAGGAGCTTCGTGAGAAAGAGAACAACTTGCC
ATTGCAGAAGAGCCAGGGAAGAGAAACTTCAGCAGGCAATAGCAATGCACACACAATTTCATGCTCCATTA

Alignment

ORF - retro_cjac_1790 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSWLFPLT-KSASSSAAGSPGGLTSLQQQKQRLIESLRNSHSSIAEIQKDVEYRLPFTINNLTININILL
          MSW.FPLT.KS.SSS.AGSPGGL.SLQ..KQ.LIES..NSHSSIAEIQKDVEYRLPF.IN.LTINI.ILL
Retrocopy MSWFFPLTTKSTSSSTAGSPGGLASLQKKKQCLIESFCNSHSSIAEIQKDVEYRLPFAINSLTINIHILL

Parental  PPQFPQEKPVISVYPPIRHHLMDKQGVYVTSPLVNNFTMHSD-LGKIIQSLLDEFWKNPPVLAPTSTAFP
          PP.FPQEKP.ISVYPPIRHHLM.KQGVY.TSPL..NFTMHSD.L.K...SLL.EFWKNPPVLAP.STAFP
Retrocopy PP*FPQEKPLISVYPPIRHHLMHKQGVYATSPLGSNFTMHSD>LEKLF-SLLNEFWKNPPVLAPISTAFP

Parental  YLYSNPSGMPPYASQGFPFLSPYSPQEANRSITSLSVADTVSSSTTSHTTAKPAAPSFGVLSNLPLPVPA
          YLYSNPSGMP.YAS..FPFL..Y.PQEAN.SI.SLSVA.TVSSSTTSHTTAKPA.PSFG.LS.LPLPVP.
Retrocopy YLYSNPSGMPSYASR-FPFLPLYPPQEANTSISSLSVANTVSSSTTSHTTAKPAPPSFGILSDLPLPVPT

Parental  MDASVPTSQNGFGYKMPDVPDAFPELSELSVSQLTDMNEQEEVLLEQFLTLPQLKQIITDKDDLVKSIEE
          MD.S.PTSQNGFGYKMPDVPDAFPELSEL.VSQ.TDMNE.E.VLLEQFLTLPQLKQIITD...LVK.IE.
Retrocopy MDISIPTSQNGFGYKMPDVPDAFPELSELGVSQPTDMNE*EKVLLEQFLTLPQLKQIITDEGELVKGIEN

Parental  LARKNL-LL-EPSLEAKRQTVLDKYELLTQMKSTFEKKMQRQHELSESCSASALQARLKVAAHEAEEESD
          LARK...LL.EPSLEA.RQTVL.KYE.LTQ..STF.KK.Q.Q.ELSESCSASALQA.LKVAA..A..E.D
Retrocopy LARKKI<LLLEPSLEAERQTVLGKYESLTQTESTFRKKKQKQQELSESCSASALQATLKVAAPKAKGEPD

Parental  NIAEDFLEGKMEIDDFLSCFMEKRTICHCRRAKEEKLQQAIAMHSQFHAPL
          NIAEDFLEGKMEID.FL..F..KRT.CHCRRA.EEKLQQAIAMH.QFHAPL
Retrocopy NIAEDFLEGKMEIDGFLRSFVRKRTTCHCRRAREEKLQQAIAMHTQFHAPL

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	19.72 RPM
SRP051959_heart	0.00 RPM	19.96 RPM
SRP051959_kidney	0.00 RPM	19.08 RPM
SRP051959_liver	0.02 RPM	15.21 RPM
SRP051959_lung	0.02 RPM	28.71 RPM
SRP051959_lymph_node	0.00 RPM	26.32 RPM
SRP051959_skeletal_muscle	0.00 RPM	21.31 RPM
SRP051959_spleen	0.08 RPM	21.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1790 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1790 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1790 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000682	2 retrocopies	retro_chof_1257, retro_chof_2124,
Callithrix jacchus	ENSCJAG00000011769	1 retrocopy	retro_cjac_1790 ,
Dipodomys ordii	ENSDORG00000014879	9 retrocopies	retro_dord_257, retro_dord_294, retro_dord_542, retro_dord_544, retro_dord_580, retro_dord_598, retro_dord_631, retro_dord_668, retro_dord_751,
Homo sapiens	ENSG00000155975	1 retrocopy	retro_hsap_3256,
Gorilla gorilla	ENSGGOG00000011650	1 retrocopy	retro_ggor_2217,
Nomascus leucogenys	ENSNLEG00000002558	1 retrocopy	retro_nleu_2687,
Pongo abelii	ENSPPYG00000018386	2 retrocopies	retro_pabe_2699, retro_pabe_2821,
Pan troglodytes	ENSPTRG00000020019	1 retrocopy	retro_ptro_2202,