RetrogeneDB ID: retro_cjac_2756

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:118189614..118190538(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG3
• Ensembl ID: ENSCJAG00000020358
• Aliases: None
• Description: autophagy related 3 [Source:HGNC Symbol;Acc:20962]

Sequence

>retro_cjac_2756
ACAATGAAGAGTAAGGCCCTGGAAGTGGTTGAGCACCTAACCCTGGTCCTCAAGGAATCAAAGTTTAAGGAAACAGATAT
AATCATCCCAGAATAGTTTGTGGCAGCTGTAGATCACTTAGTCCACCACTGTCCAACATGGCAATGGGCTACAGGGGAAG
AATTGAAAGTGAAGGCATACCTACCAACAGGCAAACAATTTTTGGTAACCAAAAATGTGCCATGCTATAAGCAGTGCAAA
CAGGTGGAACATTCAGATGAATTGGAAGCTATCATTGAAGAAGATGATGATGATGGCAGATGGGTAGATACATATGACAA
CACAGATATTACAGGAATAACCGAAGCAATGAAAGAGATCACACTGGAAAACAAAGACAGTATAAAATTTCAAGATTGCC
CAGCACTGTGTGAAGAGGTAGAAGAAGAAGGTGAAGGAGAAGCTGCAGATACAGAAGAATATGAAGAGAGTGGATTGTTG
GAAAAAGATGAGGCTACCCTAGACACAAGAAAAATAGTAGAAGCTTGTAAAGCCCAACTGATGCTGGCGGGGAAGGTGCT
ATTTTGCAAACCCAGAATTTACTACCTTTACTTCGCCTTATGATGAATAATACCCAGTCTCCGCGATTAGGGGTTGTTTG
GCTATGATGAGCAATGGCAGCAGAACGGGTTGAGCACATGTATGAAGACATCAGTCAAGATCATGTGAAGAAAATGGTGA
CCATGAAAATCACCTCATCTCCCACCACCTCCCATGTGTTCAGTTCACCCATGCAGCCATGCTGAGGTGATGAAGAACAT
CACTGAGACTGTTGCAGAAGGAGGGGGAGAACTTGGAGTTCATATACATCTTCTTACTTTCTTGAAATTTGTACAAGCTG
TCATTCCAGCAATAAAATATGACTACACGAGACACTTCATAATG

Alignment

ORF - retro_cjac_2756 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.33 %
• Parental protein coverage: 98.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  TVKGKALEVAEYLTPVLKESKFKETGVITPEEFVAAGDHLVHHCPTWQWATGEELKVKAYLPTGKQFLVT
          T.K.KALEV.E.LT.VLKESKFKET..I.PE.FVAA.DHLVHHCPTWQWATGEELKVKAYLPTGKQFLVT
Retrocopy TMKSKALEVVEHLTLVLKESKFKETDIIIPE*FVAAVDHLVHHCPTWQWATGEELKVKAYLPTGKQFLVT

Parental  KNVPCYKRCKQMEYSDELEAIIEEDDGDGGWVDTYHNTGITGITEAVKELTLENKDTIKLQDCSALCEEE
          KNVPCYK.CKQ.E.SDELEAIIEEDD.DG.WVDTY.NT.ITGITEA.KE.TLENKD.IK.QDC.ALCEE.
Retrocopy KNVPCYKQCKQVEHSDELEAIIEEDDDDGRWVDTYDNTDITGITEAMKEITLENKDSIKFQDCPALCEEV

Parental  EEEDEGEAADMEEYEESGLLETDEATLDTRKIVEACKAK-TDAGGEDAILQT-RTYDLYIT-YDKYY-QT
          EEE.EGEAAD.EEYEESGLLE.DEATLDTRKIVEACKA..TDAGGE.AILQT.R.Y.LY...YD..Y.Q.
Retrocopy EEEGEGEAADTEEYEESGLLEKDEATLDTRKIVEACKAQ<TDAGGEGAILQT>RIYYLYFA>YDE*Y>QS

Parental  PRL-WLFGYDEQRQ-PLTVEHMYEDISQDHVKKTVTI-ENH-PHLPPPPMCSVHPCRHAEVMKKIIETVA
          PRL..LFGYDEQ.Q....VEHMYEDISQDHVKK.VT..ENH.PHLPPPPMCSVHPC.HAEVMK.I.ETVA
Retrocopy PRL>GLFGYDEQWQ<AERVEHMYEDISQDHVKKMVTM<ENH<PHLPPPPMCSVHPCSHAEVMKNITETVA

Parental  EGGGELGVHMYLLIFLKFVQAVIPTIEYDYTRHFTM
          EGGGELGVH..LL.FLKFVQAVIP.I.YDYTRHF.M
Retrocopy EGGGELGVHIHLLTFLKFVQAVIPAIKYDYTRHFIM

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	0.04 RPM	18.62 RPM
SRP051959_heart	0.00 RPM	18.50 RPM
SRP051959_kidney	0.11 RPM	27.95 RPM
SRP051959_liver	0.02 RPM	42.50 RPM
SRP051959_lung	0.08 RPM	26.01 RPM
SRP051959_lymph_node	0.16 RPM	19.86 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.66 RPM
SRP051959_spleen	0.21 RPM	46.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2756 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2756 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2756 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018116	1 retrocopy	retro_amel_645,
Callithrix jacchus	ENSCJAG00000020358	1 retrocopy	retro_cjac_2756 ,
Equus caballus	ENSECAG00000011954	1 retrocopy	retro_ecab_594,
Homo sapiens	ENSG00000144848	1 retrocopy	retro_hsap_2479,
Gorilla gorilla	ENSGGOG00000006637	1 retrocopy	retro_ggor_1544,
Myotis lucifugus	ENSMLUG00000001573	1 retrocopy	retro_mluc_1025,
Macaca mulatta	ENSMMUG00000014232	1 retrocopy	retro_mmul_594,
Mustela putorius furo	ENSMPUG00000000321	2 retrocopies	retro_mputfur_1064, retro_mputfur_1614,
Nomascus leucogenys	ENSNLEG00000004302	2 retrocopies	retro_nleu_268, retro_nleu_331,
Oryctolagus cuniculus	ENSOCUG00000015651	1 retrocopy	retro_ocun_1219,
Pongo abelii	ENSPPYG00000013548	1 retrocopy	retro_pabe_1827,
Pan troglodytes	ENSPTRG00000015220	1 retrocopy	retro_ptro_1434,
Pteropus vampyrus	ENSPVAG00000009568	1 retrocopy	retro_pvam_1399,