RetrogeneDB ID: retro_cjac_3038

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:150164336..150165169(-)
• Located in intron of: ENSCJAG00000012333

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012250
• Aliases: None
• Description: None

Sequence

>retro_cjac_3038
ATGGTCACCTTTGTGGAGCTCAGTACCACCAAAGCCAAATGCCCATTGTGGGCCTGGGCACTTGGAAGTCTCCTGTCGGC
AAAGTGAAAGAAGCTGTGAAGGTGGCCATTGACGCAGGATATCGCCACATCGACTGTGCCTATGTGTATCAGAATGTGCA
TGAGGTGGGGGAAGCCATCCAAGGGAAGATCCAAGAGAAGGCTGTGAGCAGGAGGACCTCTTCATCATCAGCAAGTTGTG
GCCCACTTTCTTTGAGAGACTCTTCGTGAGGAAAGCCTGTGAGAAGACCCTCAAGGACCTGAAACTGAGCCATCTGGATG
TCTATCTTATTCACTGGCCACAAGGATTCAAGTCTGGGGATGACCTTTTTCATCCCCAGATGAAGGTAAAATGATCGATG
GAAAAGCAACGTTCTTGGATGCCTGGGAGGCCGTGGGGGAGCTGGGGGTTGCGGGGCTGGTGAAAGCCTTTGGGATTTCC
AATTTCAACCACTTCCAGATCGAGAGGCTCTTGAACAAACCTGGACTGAAATAGAAACCAGTGACTAACCAGGTTGAGTG
TCACCCCTACCTCACGCAGGAGACACTGATCCAGTAGTGCCACTCCAAGGGCATCACCGTTACAGCCTACAGCCCCCGGG
CTCTCCGGATAGACCTTGGGCCAAGCCAGAGGACCCTTCTCTGCTGGAGGATCCCACGATTAAGGAGATCGCTGCAAAGC
ACAAAAACACTGCAGCCCAGGTTCTGATCCGTTTCCATATCCAGAGGAACGTGATTGTGATCCCCCAGTCTGTCACACCA
GCACGCACTGTTGAGAACATTCAGGTCTTTGAC

Alignment

ORF - retro_cjac_3038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.63 %
• Parental protein coverage: 87.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MATFVELST-KAK-MPIVGLGTWKSPVGKVKEAVKVAIDAGYRHIDCAYVYQNEHEVGEAIQEKIQEKAV
          M.TFVELST.KAK.MPIVGLGTWKSPVGKVKEAVKVAIDAGYRHIDCAYVYQN.HEVGEAIQ.KIQEKAV
Retrocopy MVTFVELSTTKAK<MPIVGLGTWKSPVGKVKEAVKVAIDAGYRHIDCAYVYQNVHEVGEAIQGKIQEKAV

Parental  KR-EDLFIVSKLWATFFERPLVRKACEKTLKDLKLSYLDVYLIHWPQGFKSGDDIL-PKDDEGKVIAGKA
          .R.EDLFI.SKLW.TFFER..VRKACEKTLKDLKLS.LDVYLIHWPQGFKSGDD......DEGK.I.GKA
Retrocopy SR<EDLFIISKLWPTFFERLFVRKACEKTLKDLKLSHLDVYLIHWPQGFKSGDDLF<SSPDEGKMIDGKA

Parental  TFLDAWEAMEELVDAGLVKALGISNFNHFQIERLLNKPGLKYKPVTNQVECHPYLTQEKLIQYCHSKGIT
          TFLDAWEA..EL..AGLVKA.GISNFNHFQIERLLNKPGLK.KPVTNQVECHPYLTQE.LIQ.CHSKGIT
Retrocopy TFLDAWEAVGELGVAGLVKAFGISNFNHFQIERLLNKPGLK*KPVTNQVECHPYLTQETLIQ*CHSKGIT

Parental  ITAYSPL-GSPDRPWAKPEDPSLLEDPKIKEIAAKHKKTAAQVLIRFHIQRNVIVIPKSVTPARIVENIQ
          .TAYSP..GSPDRPWAKPEDPSLLEDP.IKEIAAKHK.TAAQVLIRFHIQRNVIVIP.SVTPAR.VENIQ
Retrocopy VTAYSPR<GSPDRPWAKPEDPSLLEDPTIKEIAAKHKNTAAQVLIRFHIQRNVIVIPQSVTPARTVENIQ

Parental  VFD
          VFD
Retrocopy VFD

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	27.29 RPM
SRP051959_heart	0.00 RPM	6.35 RPM
SRP051959_kidney	0.00 RPM	3.99 RPM
SRP051959_liver	0.00 RPM	210.67 RPM
SRP051959_lung	0.03 RPM	3.69 RPM
SRP051959_lymph_node	0.00 RPM	1.39 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.25 RPM
SRP051959_spleen	0.00 RPM	3.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3038 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3038 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3038 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000166	1 retrocopy	retro_chof_400,
Callithrix jacchus	ENSCJAG00000012231	14 retrocopies	retro_cjac_1140, retro_cjac_1167, retro_cjac_1718, retro_cjac_1973, retro_cjac_2550, retro_cjac_3102, retro_cjac_3143, retro_cjac_3297, retro_cjac_3692, retro_cjac_3840, retro_cjac_3872, retro_cjac_3910, retro_cjac_476, retro_cjac_621,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038 ,
Callithrix jacchus	ENSCJAG00000012872	1 retrocopy	retro_cjac_1688,
Callithrix jacchus	ENSCJAG00000013633	2 retrocopies	retro_cjac_3093, retro_cjac_3334,
Erinaceus europaeus	ENSEEUG00000004422	1 retrocopy	retro_eeur_681,
Echinops telfairi	ENSETEG00000006005	3 retrocopies	retro_etel_1055, retro_etel_1643, retro_etel_748,
Homo sapiens	ENSG00000198074	1 retrocopy	retro_hsap_581,
Macaca mulatta	ENSMMUG00000013098	2 retrocopies	retro_mmul_1357, retro_mmul_2455,
Mus musculus	ENSMUSG00000029762	1 retrocopy	retro_mmus_627,
Mus musculus	ENSMUSG00000052131	1 retrocopy	retro_mmus_2860,
Mus musculus	ENSMUSG00000061758	1 retrocopy	retro_mmus_1490,
Nomascus leucogenys	ENSNLEG00000013088	1 retrocopy	retro_nleu_801,
Pongo abelii	ENSPPYG00000018018	1 retrocopy	retro_pabe_606,
Pan troglodytes	ENSPTRG00000019718	1 retrocopy	retro_ptro_428,
Rattus norvegicus	ENSRNOG00000009734	3 retrocopies	retro_rnor_2380, retro_rnor_2588, retro_rnor_657,
Sorex araneus	ENSSARG00000001396	1 retrocopy	retro_sara_608,