RetrogeneDB ID: retro_cjac_2304

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:190790882..190791836(-)
• Located in intron of: ENSCJAG00000002032

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000009147
• Aliases: None
• Description: None

Sequence

>retro_cjac_2304
TTAGATAAACTCAGCATTGACAGCATCATCCAACAGCTGCTGGAAGTGAGAGGATCCAAACCCGGTAAGAATCTCCAGCT
TCAGGAGAATGAAATCAGGAGACTGTGCTTAAAGTCTCATGAGATCTTTCTCAGTCAGCCTATCCTACTAGAACTTGAAG
CACCACTCAAAATACGTGGTGGCATCCATGGTCAATACTGTGATTTGCTGAGACTTTTTGAGTACGGTGGTTTCCCGCCA
GAAAGCAACTACCTGTTTCTTGGGGACTCTGTGGACAGGAGAAAGCAGTCATTGGAGACAGTCTGCCTCTTGCTGGCCTA
CAAAATCAAATATCCTGAGAATTTTTTTCTTCTCAGAGGGAACCATGAATGTGCCAGCATCAACAGAATTTATGGATTTT
CTGATGCATGTAAAAGAAGTTACAACATTAAACTATGGAAAACTTTCACAGACTGTTTTAATTTACCTATAGCAGCCATC
GTGGATGAGAAGATATTCTGCTGTCGTGGAGGTTTATCACCAGATCTTCAATCTATGGAGCAGATTCGGCGAATTATGCG
ACCAACTGATGTACCAGATCGGGGTCTTCTCTGTGATCTTTTGTGGCCTGACCCTGATAAAGATGTCTTAGGGTGGGGTA
AAAATGACAGAGGAGTGTCCTTCACATTTGCTGCAGAAGTGGTTGCAAAATTTCTCCATAAGCATGATTTGGATCTTATA
TGTAGAGCCCATCAGGTGGTTGAAGATGGATATGAATTTTTTGCAAAGAGGCAGTTGGTCACTCTGTTTTCTGCACCCAA
TTGTGGAGAGTTTGACAATGCAGGTGCCATGATGAGTGTGAACGAAACACTAATGTGTTCTTTTCAGATTTTAAAGTCTG
CAGAGAAAAAGAAGCCAAATGCCACGAGACCTGTAACACCTCCAAGGGATATGATCACAAAACAAGCAAAGAAA

Alignment

ORF - retro_cjac_2304 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.5 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLL
          LDKL.IDSIIQ.LLEVRGSKPGKN.QLQENEIR.LCLKS.EIFLSQPILLELEAPLKI.G.IHGQY.DLL
Retrocopy LDKLSIDSIIQQLLEVRGSKPGKNLQLQENEIRRLCLKSHEIFLSQPILLELEAPLKIRGGIHGQYCDLL

Parental  RLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRR
          RLFEYGGFPPESNYLFLGD.VDR.KQSLET.CLLLAYKIKYPENFFLLRGNHECASINRIYGF.D.CKR.
Retrocopy RLFEYGGFPPESNYLFLGDSVDRRKQSLETVCLLLAYKIKYPENFFLLRGNHECASINRIYGFSDACKRS

Parental  YNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDV
          YNIKLWKTFTDCFN.LPIAAIVDEKIFCC.GGLSPDLQSMEQIRRIMRPTDVPD.GLLCDLLW.DPDKDV
Retrocopy YNIKLWKTFTDCFN-LPIAAIVDEKIFCCRGGLSPDLQSMEQIRRIMRPTDVPDRGLLCDLLWPDPDKDV

Parental  LGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMM
          LGWG.NDRGVSFTF.AEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPN.CGEFDNAGAMM
Retrocopy LGWGKNDRGVSFTFAAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPN-CGEFDNAGAMM

Parental  SVDETLMCSFQILKPAEKKKPNATRPVTPPRGMITKQAKK
          SV.ETLMCSFQILK.AEKKKPNATRPVTPPR.MITKQAKK
Retrocopy SVNETLMCSFQILKSAEKKKPNATRPVTPPRDMITKQAKK

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	0.87 RPM	63.72 RPM
SRP051959_heart	0.60 RPM	62.29 RPM
SRP051959_kidney	0.69 RPM	51.38 RPM
SRP051959_liver	0.35 RPM	41.91 RPM
SRP051959_lung	0.70 RPM	67.66 RPM
SRP051959_lymph_node	1.00 RPM	105.75 RPM
SRP051959_skeletal_muscle	0.13 RPM	62.13 RPM
SRP051959_spleen	1.13 RPM	93.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2304 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2304 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2304 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013861	1 retrocopy	retro_amel_1721,
Bos taurus	ENSBTAG00000011198	2 retrocopies	retro_btau_6, retro_btau_960,
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000000983	1 retrocopy	retro_cjac_923,
Callithrix jacchus	ENSCJAG00000009147	7 retrocopies	retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304 , retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Dipodomys ordii	ENSDORG00000010484	2 retrocopies	retro_dord_260, retro_dord_261,
Equus caballus	ENSECAG00000017228	1 retrocopy	retro_ecab_853,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065,
Myotis lucifugus	ENSMLUG00000010661	2 retrocopies	retro_mluc_15, retro_mluc_2217,
Mus musculus	ENSMUSG00000004455	5 retrocopies	retro_mmus_2274, retro_mmus_2968, retro_mmus_3418, retro_mmus_851, retro_mmus_925,
Oryctolagus cuniculus	ENSOCUG00000009275	2 retrocopies	retro_ocun_1232, retro_ocun_665,
Pan troglodytes	ENSPTRG00000005448	1 retrocopy	retro_ptro_2435,
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Tupaia belangeri	ENSTBEG00000013852	4 retrocopies	retro_tbel_1710, retro_tbel_2116, retro_tbel_2311, retro_tbel_4450,
Vicugna pacos	ENSVPAG00000008411	1 retrocopy	retro_vpac_540,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,