RetrogeneDB ID: retro_cjac_115

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:57870441..57871746(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023324
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011679
• Aliases: None
• Description: None

Sequence

>retro_cjac_115
ATGGCCATACAGAAAGTCTTTGCTCGGGAAATCCTGGACTCCAGGTGCAACCCCACAGTGGAGGTGGACCTGCACACAGC
CAAGGGCCGATTCCGAGCAGCTGTGCCCAGTGGGGCTTCCACGGGTATCTATGAAGTTCTGGAACTAAGAGATGGAGACA
AAGCCCACTATCTGGGGAAAGGAGTCCTGAAGGCTGTGGAACACATCAACAAGACTCTAGGCCCTTCTTTGCTGGAAAAG
AAACTAAGTGTTGTGGATCAAGAAAAAGCTGACAAATTTATGATTGAGCTGGATGGGACCGAGAATAAGTCCAAGTTTGG
GGCCAATGCCATCCTGGGCGTGTCCTTGGCCGTGTGTAAGGCGGGAGCAGCTGAGAAGGGGGTCCCCCTTTACCGCCACA
TTGCAGATCTTGCTGGGAACCCTGACCTCATACTCCCAGTGCCAGCTTTCAACATGATCAACGGGGGCTCCCATGCTGGA
AACAAGCTGGCCATGCAGGAGTTCATGATTCTGCCTGTGGGAGCCAGCTCCTTCAAGGAAGCCATGCGCATTGGTGCTGA
GGTCTACCACCACCTCAAGGGGGTTATCAAGGCCAAGTATGGGAAGGATGCCACCAATGTGGGTGATGAAGGTGGCTTCG
CACCCAACATCCTGGAGAACAGTGAGGCCCTAGAGCTGCTGAAGACAGCCCTCCAGGCAGCTGGTTATCCAGACAAGGTG
GTGATCGGCATGGATGTGGCAGCCTCTGAGTTCTATCGCAATGGGAAGTACGATCTTGACTTCAAGTCACCTGATGATCC
CGCACGGCACATCACTGGGGAGAAGCTTGGAGAGCTGTATAAGAGCTTCATCAAGAACTACCCTGTGGTCTCCATCGAGG
ACCCCTTTGACCAGGATGACTGGGCCACTTGGACCTCGTTCCTCTCGAGAGTGAACATCCAGATTGTGGGGTATGACCTG
ACAGTCACCAACCCCAAGAGGATTGCCCAGGCCGTTGAGAAGAAGGCCTGTAACTGTCTGCTGCTGAAGGTCAACCAGAT
GGGCTCGGTGACTGAATCGATCCAGGCGTGCAAACTTGCTCTGTCTAACGGCTGGGGAGTGATGGTGAGCCATCGCTCTG
GGGAGACTGAGGACACATTCATTGCTGACCTTGTGGTGGGACTCTGCACAGGACAGATCAAGACTGGCGCCCCCTGTCGC
TCAGAGCGTCTGGCCAAATACAACCAACTCATGAGGATCGAGGAGGCTCTTGGGGACAAGGCTATATTTGCTGGACGAAA
GTTCCGCCACCCGAAGGCCAAGTGA

Alignment

ORF - retro_cjac_115 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMQKIFAREILDSRGNPTVEVDLHTAKGRFRAAVPSGASTGIYEALELRDGDKARYLGKGVLKAVEHIN
          MA.QK.FAREILDSR.NPTVEVDLHTAKGRFRAAVPSGASTGIYE.LELRDGDKA.YLGKGVLKAVEHIN
Retrocopy MAIQKVFAREILDSRCNPTVEVDLHTAKGRFRAAVPSGASTGIYEVLELRDGDKAHYLGKGVLKAVEHIN

Parental  KTLGPALLEKKLSVVDQEKVDKFMIELDGTENKSKFGANAILGVSLAVCKAGAAEKGVPLYRHIADLAGN
          KTLGP.LLEKKLSVVDQEK.DKFMIELDGTENKSKFGANAILGVSLAVCKAGAAEKGVPLYRHIADLAGN
Retrocopy KTLGPSLLEKKLSVVDQEKADKFMIELDGTENKSKFGANAILGVSLAVCKAGAAEKGVPLYRHIADLAGN

Parental  PDLILPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFKEAMRIGAEVYHHLKGVIKAKYGKDATNVGDE
          PDLILPVPAFN.INGGSHAGNKLAMQEFMILPVGASSFKEAMRIGAEVYHHLKGVIKAKYGKDATNVGDE
Retrocopy PDLILPVPAFNMINGGSHAGNKLAMQEFMILPVGASSFKEAMRIGAEVYHHLKGVIKAKYGKDATNVGDE

Parental  GGFAPNILENNEALELLKTAIQAAGYPDKVVIGMDVAASEFYRNGKYDLDFKSPDDPARHITGEKLGELY
          GGFAPNILEN.EALELLKTA.QAAGYPDKVVIGMDVAASEFYRNGKYDLDFKSPDDPARHITGEKLGELY
Retrocopy GGFAPNILENSEALELLKTALQAAGYPDKVVIGMDVAASEFYRNGKYDLDFKSPDDPARHITGEKLGELY

Parental  KSFIKNYPVVSIEDPFDQDDWATWTSFLSGVNIQIVGDDLTVTNPKRIAQAVEKKACNCLLLKVNQIGSV
          KSFIKNYPVVSIEDPFDQDDWATWTSFLS.VNIQIVG.DLTVTNPKRIAQAVEKKACNCLLLKVNQ.GSV
Retrocopy KSFIKNYPVVSIEDPFDQDDWATWTSFLSRVNIQIVGYDLTVTNPKRIAQAVEKKACNCLLLKVNQMGSV

Parental  TESIQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCLSERLAKYNQLMRIEEALGDK
          TESIQACKLA.SNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPC.SERLAKYNQLMRIEEALGDK
Retrocopy TESIQACKLALSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEALGDK

Parental  AIFAGRKFRNPKAK
          AIFAGRKFR.PKAK
Retrocopy AIFAGRKFRHPKAK

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	0.51 RPM
SRP051959_heart	3.46 RPM	77.93 RPM
SRP051959_kidney	0.04 RPM	0.64 RPM
SRP051959_liver	0.00 RPM	0.37 RPM
SRP051959_lung	0.08 RPM	1.50 RPM
SRP051959_lymph_node	0.02 RPM	1.00 RPM
SRP051959_skeletal_muscle	74.01 RPM	1746.60 RPM
SRP051959_spleen	0.02 RPM	0.38 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_115 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_115 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_115 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015802	2 retrocopies	retro_cfam_1010, retro_cfam_2134,
Callithrix jacchus	ENSCJAG00000000359	4 retrocopies	retro_cjac_1963, retro_cjac_2238, retro_cjac_3891, retro_cjac_438,
Callithrix jacchus	ENSCJAG00000011679	2 retrocopies	retro_cjac_115 , retro_cjac_177,
Dasypus novemcinctus	ENSDNOG00000011654	2 retrocopies	retro_dnov_1712, retro_dnov_75,
Macropus eugenii	ENSMEUG00000007915	25 retrocopies	retro_meug_1019, retro_meug_1341, retro_meug_1483, retro_meug_1540, retro_meug_1566, retro_meug_1605, retro_meug_170, retro_meug_1701, retro_meug_1743, retro_meug_1869, retro_meug_1905, retro_meug_1929, retro_meug_2026, retro_meug_2190, retro_meug_235, retro_meug_269, retro_meug_578, retro_meug_607, retro_meug_637, retro_meug_803, retro_meug_820, retro_meug_906, retro_meug_965, retro_meug_973, retro_meug_976,
Rattus norvegicus	ENSRNOG00000004078	1 retrocopy	retro_rnor_2228,
Tupaia belangeri	ENSTBEG00000002346	5 retrocopies	retro_tbel_1514, retro_tbel_3080, retro_tbel_3130, retro_tbel_4230, retro_tbel_4383,
Tarsius syrichta	ENSTSYG00000007066	7 retrocopies	retro_tsyr_1019, retro_tsyr_1157, retro_tsyr_1626, retro_tsyr_1917, retro_tsyr_2043, retro_tsyr_52, retro_tsyr_534,