RetrogeneDB ID: retro_cjac_576

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:82915450..82916361(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNW1
• Ensembl ID: ENSCJAG00000016947
• Aliases: None
• Description: None

Sequence

>retro_cjac_576
CCTTCTCCTCCTGCACCTGTCATGCATTCTCCTAGCCGAAAGATTCCTCCTTGTATTTCTAACTGGAAAAATGCAAAGGG
TTAAACAATTCCATTAGACAAACGTCTGGCTGCTGATGGAAGAGGACTACAGACAGTACACATAAATGAAAATTTTGCCA
AACTGGCCAAAGCCCTCTACATTGCTGATTGGAAGGCTCATGAAGCTGTGGAAATGCATGCCCAAGTAGAGAGAAAAATG
GCTCAAAAAGAAAAGGAAAAACATGAAGAGAAACTTAGAGAAATGGCCCAGAAAGCCAGGGAGAGAAGAGCTGGGATCAA
AACTCCTGTGGAAAAAGAGGATGGGGAGGCACGTGAAAGGGATGAAATCTGGCATGACAGGTGAAAAGAGAGACAGCATG
ACCAGAATCTTTCCAGGGCAGCTCCTGATAAGAGGTCGAAACTTCAGAGAAACGAAAATCGGAATATCAGTGAGGTCATT
GCTCTCAGTGTTCCTAATCCTCGGACTTCCAATGAAGTTCAGTACGACCAAAGGCTCTTCAACCAATCCAAGGGTATGGA
CAGTGGATTTGCAGGTGGAGAAGATGACATTTATAATGTTTATGATCAAGCCTGGAGAGGTGGTAAATATATGGCCCAGA
GTATTTATAAGCCCAGTAAAAATCTGGAGAAGGACATGTATGGTGATGACCTAGAAGCCAGAATAAAGACCAACAGATTT
GTTCCCAACAAGGAGTTTTCTGGTTCAGACCATAGGCAGAGACGCCGAGAAGGACCAGTTCAGTTTGAGGAAGATCCTTT
TGGTTTGGACAAGTTTTGGAAGAAGCCAAACAGCATGGTGGCTCTAAAAGACCCTCAGATAGCAGCCACCCCAAGGAACA
TGAGCATGAAGGCAAGAAGAGGAGGAAAAAG

Alignment

ORF - retro_cjac_576 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.84 %
• Parental protein coverage: 56.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHINENFAKLAEALYIADRKAREAV
          PS....V......KIPPCISNWKNAKG.TIPLDKRLAADGRGLQTVHINENFAKLA.ALYIAD.KA.EAV
Retrocopy PSPPAPVMHSPSRKIPPCISNWKNAKG*TIPLDKRLAADGRGLQTVHINENFAKLAKALYIADWKAHEAV

Parental  EMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEARERDEIRHDRRKERQHDRNLSRA
          EM.AQVERKMAQKEKEKHEEKLREMAQKARERRAGIKT.VEKEDGEARERDEI.HDR.KERQHD.NLSRA
Retrocopy EMHAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTPVEKEDGEARERDEIWHDR*KERQHDQNLSRA

Parental  APDKRSKLQRNENRDISEVIALGVPNPRTSNEVQYDQRLFNQSKGMDSGFAGGEDEIYNVYDQAWRGGKD
          APDKRSKLQRNENR.ISEVIAL.VPNPRTSNEVQYDQRLFNQSKGMDSGFAGGED.IYNVYDQAWRGGK.
Retrocopy APDKRSKLQRNENRNISEVIALSVPNPRTSNEVQYDQRLFNQSKGMDSGFAGGEDDIYNVYDQAWRGGKY

Parental  MAQSIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSGSDRRQRGREGPVQFEEDPFGLDKF-LEEAKQH
          MAQSIY.PSKNL.KDMYGDDLEARIKTNRFVP.KEFSGSD.RQR.REGPVQFEEDPFGLDKF.LEEAKQH
Retrocopy MAQSIYKPSKNLEKDMYGDDLEARIKTNRFVPNKEFSGSDHRQRRREGPVQFEEDPFGLDKF<LEEAKQH

Parental  GGSKRPSDSSRPKEHEHEGKKRRKE
          GGSKRPSDSS.PKEHEHEGKKRRK.
Retrocopy GGSKRPSDSSHPKEHEHEGKKRRKK

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	0.04 RPM	26.51 RPM
SRP051959_heart	0.02 RPM	32.27 RPM
SRP051959_kidney	0.02 RPM	40.80 RPM
SRP051959_liver	0.06 RPM	25.21 RPM
SRP051959_lung	0.07 RPM	43.68 RPM
SRP051959_lymph_node	0.05 RPM	38.10 RPM
SRP051959_skeletal_muscle	0.07 RPM	34.24 RPM
SRP051959_spleen	0.02 RPM	39.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_576 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_576 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_576 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003976	2 retrocopies	retro_amel_163, retro_amel_912,
Canis familiaris	ENSCAFG00000030409	1 retrocopy	retro_cfam_195,
Callithrix jacchus	ENSCJAG00000016947	2 retrocopies	retro_cjac_2932, retro_cjac_576 ,
Dipodomys ordii	ENSDORG00000012380	3 retrocopies	retro_dord_693, retro_dord_781, retro_dord_782,
Felis catus	ENSFCAG00000001637	1 retrocopy	retro_fcat_635,
Loxodonta africana	ENSLAFG00000003482	2 retrocopies	retro_lafr_474, retro_lafr_787,
Myotis lucifugus	ENSMLUG00000005228	2 retrocopies	retro_mluc_387, retro_mluc_805,
Monodelphis domestica	ENSMODG00000005252	1 retrocopy	retro_mdom_1841,
Mustela putorius furo	ENSMPUG00000008724	1 retrocopy	retro_mputfur_551,
Mus musculus	ENSMUSG00000021039	2 retrocopies	retro_mmus_1022, retro_mmus_387,
Ochotona princeps	ENSOPRG00000007568	1 retrocopy	retro_opri_737,
Pongo abelii	ENSPPYG00000006031	1 retrocopy	retro_pabe_454,
Sorex araneus	ENSSARG00000002279	3 retrocopies	retro_sara_403, retro_sara_568, retro_sara_727,
Taeniopygia guttata	ENSTGUG00000012340	2 retrocopies	retro_tgut_15, retro_tgut_30,
Tarsius syrichta	ENSTSYG00000010951	1 retrocopy	retro_tsyr_1871,