RetrogeneDB ID: retro_cjac_3279

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:20475779..20476582(-)
• Located in intron of: ENSCJAG00000018934

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK1G3
• Ensembl ID: ENSCJAG00000017348
• Aliases: None
• Description: None

Sequence

>retro_cjac_3279
ACCAGCTCGGGGGTCCTGATGGTGGGCCCCAACTTCCGCATCGGCAAGAAGATCGGCTGTGGCAACTTCGGGGAGCTCCG
CCTAGGAAAGAATCTCTTTACAAATAAATAAGTGGCTATCAAATGGGAGCCGATTAAGTCACGGGCCCCACAGCTGCACT
TGGAGTAGCAGCTCTACAAGCAGCTCAGTGCCACAGAGGGCGTCCCTCAGGTCGACTACTTCGGCCAGTGTGGGCGGTAC
AACGCCATGGTGCTGGAGCTGCTGGGGCCCAGCCTGGAGGACCTGTTTGACCTGTGTGACCGGACCTTGACGCTCAAGAC
GGTGCTGATGATCGCCATCCAGCTGATCACGCGCATGGAGTACTGCACACCGAGAGCCTCATCTACCCGGACATGAAGCC
CGAGAACTTCCTGGTGGGCCGCCCAGGGACCAAGCAGCAGCACGCCATCCACATCATTGACTTCGGGCTGGCCAAGGAGT
ACATCGACCCCAGACCAAGAAGCACATCCCTTACCGCGAGCACAAGAGCCTGACAGGCACAGCGCGCTACATGAGCATCA
ACACGCACCTGGGCAAGGACGTGTTGCCACGACGACCTGGAGGCGCTGAGCCACATGTTCATGTACTTCCTGCGCGGCAG
CCTCCCCTGGCAGGGGTTCAAGGCCGACATGCTCAAGGAGCGGTACCAGAAGATTGGGGACATCAAACGCGCCACGCCCA
TTGAGGTGCTCTGCGAGAATTTCCCAGAGGAGATGGCCATGTACCTGTGCTACGTGCGGCACCTAGACTTCTTCGAGAAG
CCC

Alignment

ORF - retro_cjac_3279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72. %
• Parental protein coverage: 59.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SSSGVLMVGPNFRVGKKIGCGNFGELRLGKNLYTNEYVAIKLEPMKSRAPQLHLEYRFYKQLGSGDGIPQ
          .SSGVLMVGPNFR.GKKIGCGNFGELRLGKNL.TN..VAIK.EP.KSRAPQLHLE...YKQL....G.PQ
Retrocopy TSSGVLMVGPNFRIGKKIGCGNFGELRLGKNLFTNK*VAIKWEPIKSRAPQLHLE*QLYKQLSATEGVPQ

Parental  VYYFGPCGKYNAMVLELLGPSLEDLFDLCDRTFSLKTVLMIAIQLTKISRMEY-VHSKNLIYRDVKPENF
          V.YFG.CG.YNAMVLELLGPSLEDLFDLCDRT..LKTVLMIAIQL..I.RMEY..H...LIY.D.KPENF
Retrocopy VDYFGQCGRYNAMVLELLGPSLEDLFDLCDRTLTLKTVLMIAIQL--ITRMEY<LHTESLIYPDMKPENF

Parental  LIGRPGNKTQQVIHIIDFGLAKEYID-PETKKHIPYREHKSLTGTARYMSINTHLGKEQSRRDDLEALGH
          L.GRPG.K.Q..IHIIDFGLAKEYID.P.TKKHIPYREHKSLTGTARYMSINTHLGK....R....A..H
Retrocopy LVGRPGTKQQHAIHIIDFGLAKEYID<PQTKKHIPYREHKSLTGTARYMSINTHLGKDVLPRRPGGAEPH

Parental  MFMYFLR-GSLPWQGLKADTLKERYQKIG-DTKRATPIEVLCENFPEEMATYLRYVRRLDFFEKP
          ......R....P..G.............G.D.KRATPIEVLCENFPEEMA.YL.YVR.LDFFEKP
Retrocopy VHVLPAR<AASPGRGSRPTCSRSGTRRLG<DIKRATPIEVLCENFPEEMAMYLCYVRHLDFFEKP

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	0.24 RPM	21.63 RPM
SRP051959_heart	0.53 RPM	16.15 RPM
SRP051959_kidney	0.31 RPM	22.12 RPM
SRP051959_liver	0.28 RPM	8.82 RPM
SRP051959_lung	0.49 RPM	20.61 RPM
SRP051959_lymph_node	0.46 RPM	23.79 RPM
SRP051959_skeletal_muscle	0.31 RPM	6.97 RPM
SRP051959_spleen	0.55 RPM	26.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3279 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3279 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3279 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017550	1 retrocopy	retro_btau_1659,
Callithrix jacchus	ENSCJAG00000017348	2 retrocopies	retro_cjac_2695, retro_cjac_3279 ,
Callithrix jacchus	ENSCJAG00000021121	1 retrocopy	retro_cjac_2680,
Macaca mulatta	ENSMMUG00000006646	1 retrocopy	retro_mmul_1040,
Mus musculus	ENSMUSG00000073563	1 retrocopy	retro_mmus_3454,
Otolemur garnettii	ENSOGAG00000011587	1 retrocopy	retro_ogar_246,
Rattus norvegicus	ENSRNOG00000016677	1 retrocopy	retro_rnor_2189,