RetrogeneDB ID: retro_cjac_3935

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286328.1:1172..1740(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000004107
• Aliases: None
• Description: None

Sequence

>retro_cjac_3935
TGCTAGACGTCCGTCCTGCCGGTCCGATTCCTGGGCATCTCCCCTCGGCAAATTCCAGTAGATACTAACTTCCACTCTGC
CTCTTTATCTGACACAGACCATCCACGAGTCTTAATTACAGGGGGTCTTGGCCAGCTGGGAGTGGGGCTTGCTAATCTTT
TGAGGAAACGATTCGGGAAGGACAGTGTGATTTTGTCTGACATAAAGAAACCACCGATCATGTCTTTCACAGTGGTCCAT
TCATTTATTCTGATATCTTGGATTACAAGAATCTTCGGGAGATCGTGGTAAACAACCGCATCACCTGGCTGTTTCATTAC
AACGCCTTGCTCAGCGCCATTGGAGAAGCGAATGGTTCCCTGGCGAGAGCAGTGAATGTAACTGGCCTGCATAACTGGGC
GTCGCTGCGGAACAGTCTGCGATTGTTTGTACCTAGCACGATCGGAGCTTTTGGACCCACCTCTCCCCGGAACCAACCAC
CGATCTCTGTATTCAGAGACCCAGGACCATCTAAGGACTGTCCAAGATCCACGCGGAGCTCATGGGAGAATATTATCATT
ACCGGTAT

Alignment

ORF - retro_cjac_3935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.54 %
• Parental protein coverage: 83.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CWTSVLPVRFLGISPRQIPADANFHSASFSDTDHPRVLITGGLGQLGVGLANLLRKRFGKDSVILSDIKK
          C.TSVLPVRFLGISPRQIP.D.NFHSAS.SDTDHPRVLITGGLGQLGVGLANLLRKRFGKDSVILSDIKK
Retrocopy C*TSVLPVRFLGISPRQIPVDTNFHSASLSDTDHPRVLITGGLGQLGVGLANLLRKRFGKDSVILSDIKK

Parental  PP-DHVFHSGPFIYSDILDYKSLREIVVNKRITWLFHYSALLSAVGEANVSLARAVNITGLHNILDVAAE
          PP.DHVFHSGPFIYSDILDYK.LREIVVN.RITWLFHY.ALLSA.GEAN.SLARAVN.TGLHN.......
Retrocopy PP<DHVFHSGPFIYSDILDYKNLREIVVNNRITWLFHYNALLSAIGEANGSLARAVNVTGLHNW--ASLR

Parental  HSLRLFVPSTIGAFGPTSPRN-PAPDLCIQRPRTIYGVSKVHAELMGETMQSRF
          .SLRLFVPSTIGAFGPTSPRN.P..DLCIQRPRTI.G.SK.HAELMGE....R.
Retrocopy NSLRLFVPSTIGAFGPTSPRN<PTTDLCIQRPRTI*GLSKIHAELMGEYYHYRY

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	0.02 RPM	0.20 RPM
SRP051959_heart	0.02 RPM	0.42 RPM
SRP051959_kidney	0.40 RPM	11.09 RPM
SRP051959_liver	0.00 RPM	0.24 RPM
SRP051959_lung	0.00 RPM	0.68 RPM
SRP051959_lymph_node	0.02 RPM	0.57 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.31 RPM
SRP051959_spleen	0.04 RPM	0.48 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3935 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3935 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3935 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002579	1 retrocopy	retro_chof_1442,
Callithrix jacchus	ENSCJAG00000004107	1 retrocopy	retro_cjac_3935 ,
Mus musculus	ENSMUSG00000021953	1 retrocopy	retro_mmus_1962,