RetrogeneDB ID: retro_cjac_3180

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:9649168..9649760(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000020030
• Aliases: None
• Description: None

Sequence

>retro_cjac_3180
ATGGACCCCCTGTACCAGCAAACGCACAAGCAGGTCCACGAGATCCAGTCTTGCATGGGACGCCTGGAGACTGCAGACAA
GCAGTCTGTGCATTCAGTAGAAAACAAAATCCAAGCAAGCATAGACCAGATAGTCAGCCGTCTAGAACACCTGGAGATTT
TGTCCAGCAAGGAGCCTCCTAACCAAAGGCAGAATGCCAAACTTTGGGTTGACCAGTTAAAGTATGATGTCCAGCACCTA
CAGACTGCTGTCAGAAACTTCCAGCATCAGCGCCATGCAAGGGAACAGTAGGAGAGACAGAGAGAAGAGCTTCTGTCTCG
AACCTTCACCGCTAACGACTCTCACACCGCCATACCAATGGAGGAATCACTGCAGTTTAACTCTCCCTCAGAAAATTCAT
CAGTGATTAAATGAGGCATGGACGACCTCATTTTACATGGGCACAATATTTTAGATGGACTGAGGACCCAGAGACTGACC
TTGAAGGGGACTCAAGAAGATCCCTGACATTGCCAACACGATGGGCTTGTCCAACTCAGTGGTGTGGCTCATGGAGAAGC
GGGCTTTCCAGAACAAGTACTTCATGATCGGC

Alignment

ORF - retro_cjac_3180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.5 %
• Parental protein coverage: 91.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDTLYQQTHKQVHEIQSRMGRLETADKQSVHLVENEIQASIDQIFSHLERLEILSSKEPPNKRQNAKLRV
          MD.LYQQTHKQVHEIQS.MGRLETADKQSVH.VEN.IQASIDQI.S.LE.LEILSSKEPPN.RQNAKL.V
Retrocopy MDPLYQQTHKQVHEIQSCMGRLETADKQSVHSVENKIQASIDQIVSRLEHLEILSSKEPPNQRQNAKLWV

Parental  DQLKYDVQHLQTALRNFQHRRHAREQQERQREELLSRTFTTNDSDTTIPMDESLQFNSSLQK---IHHGV
          DQLKYDVQHLQTA.RNFQH.RHAREQ.ERQREELLSRTFT.NDS.T.IPM.ESLQFNS.......I..G.
Retrocopy DQLKYDVQHLQTAVRNFQHQRHAREQ*ERQREELLSRTFTANDSHTAIPMEESLQFNSPSENSSVIK*GM

Parental  DDLILDGHNILDGLRNQRLT-LKGTQ-KKILDIANMLGLSNTVMRLIEKRAFQDKYFMIG
          DDLIL.GHNILDGLR.QRLT.L.G...KKI.DIAN..GLSN.V..L.EKRAFQ.KYFMIG
Retrocopy DDLILHGHNILDGLRTQRLT<LEGDS<KKIPDIANTMGLSNSVVWLMEKRAFQNKYFMIG

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	7.08 RPM
SRP051959_heart	0.00 RPM	8.26 RPM
SRP051959_kidney	0.00 RPM	9.98 RPM
SRP051959_liver	0.00 RPM	9.47 RPM
SRP051959_lung	0.07 RPM	9.16 RPM
SRP051959_lymph_node	0.05 RPM	10.14 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.05 RPM
SRP051959_spleen	0.00 RPM	8.70 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3180 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3180 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3180 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013419	1 retrocopy	retro_cfam_1351,
Callithrix jacchus	ENSCJAG00000020030	1 retrocopy	retro_cjac_3180 ,
Felis catus	ENSFCAG00000028951	1 retrocopy	retro_fcat_678,
Myotis lucifugus	ENSMLUG00000002709	1 retrocopy	retro_mluc_752,
Macaca mulatta	ENSMMUG00000018689	1 retrocopy	retro_mmul_367,
Nomascus leucogenys	ENSNLEG00000004922	1 retrocopy	retro_nleu_1211,
Pan troglodytes	ENSPTRG00000009323	1 retrocopy	retro_ptro_1290,
Ictidomys tridecemlineatus	ENSSTOG00000016069	2 retrocopies	retro_itri_1790, retro_itri_270,