RetrogeneDB ID: retro_cjac_490

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:185838315..185838958(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRA1
• Ensembl ID: ENSCJAG00000016613
• Aliases: None
• Description: steroid receptor RNA activator 1 [Source:HGNC Symbol;Acc:11281]

Sequence

>retro_cjac_490
GGCAACAAGGAGCGAGGTTGGAACGACCCGCCACAGTTCTCATACGGGCTGCAGAGCCAGGCCGGCAGACCCAGGCACGC
ACTACTCACCAAGAGGGTCGCCACACCCCAGGATAGATCCCCCAGAGTCCCAGCCTCAGAGACTTCTCCTGGGCCTCCCT
CAATGGGGCCTCCAGCTCCTTCAAGTAAGGCTCCCAGGTCCTCACCTGTGGGGAGTGATCCTGCCTCTGGTGTGGAGCCC
ACAAGTTTCCCAGTTGAGTCTGAGGCTCTGATGGAAGATGAGCTGAGACCTTTGGAACAGGCATTGGAAGACTGCCGTGG
CCACACAAAGAAACAAGAATGTGATGACATCAGCCGACGCCTGGCACTGCTGCAGGAACAGTGGGCTGGAGGAAAGTTGT
CAATACCTGTAAAGAATAGAATGGCTCTACTGGTACAAGAGCTTTCAACCCACCAGTGGGATGCAACAGATGGCATCCAC
TGCTCACTCATGGTTGACCATGTGACTGAGGCCAATCAGTGGATGGAGTTAAAAGATTAATTGCGGAAAGAAGAGTCTGT
TTTCAGAGGAGGCAGCCAATGAAGAGAAATCTGCAGCCACAGCTGAGAAGAACCAGACCATACCGGGCTTCCAGCGGGCG
CCA

Alignment

ORF - retro_cjac_490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.11 %
• Parental protein coverage: 91.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GNKERGWNDPPQFSYGLQTQAGGTRRTLLTKRVAAPQDGSPRVPASETSPGPPPMGPPPPSSKAPRSPPV
          GNKERGWNDPPQFSYGLQ.QAG..R..LLTKRVA.PQD.SPRVPASETSPGPP.MGPP.PSSKAPRS.PV
Retrocopy GNKERGWNDPPQFSYGLQSQAGRPRHALLTKRVATPQDRSPRVPASETSPGPPSMGPPAPSSKAPRSSPV

Parental  GSDPASGVEP-SFPVESEALMEDVLRPLEQALEDCRGHTKKQVCDDISRRLALLQEQWAGGKLSIPVKKR
          GSDPASGVEP.SFPVESEALMED.LRPLEQALEDCRGHTKKQ.CDDISRRLALLQEQWAGGKLSIPVK.R
Retrocopy GSDPASGVEPTSFPVESEALMEDELRPLEQALEDCRGHTKKQECDDISRRLALLQEQWAGGKLSIPVKNR

Parental  MTLLVQELSNHQWDAADDIHRSLMVDHVTEVSQWMVGVKRLIAEKRSLF-SEEAANEEKSAATPEKNQTI
          M.LLVQELS.HQWDA.D.IH.SLMVDHVTE..QWM...K.......S.F..E.A..E.KSAAT.EKNQTI
Retrocopy MALLVQELSTHQWDATDGIHCSLMVDHVTEANQWM-ELKD*LRKEESVF>EEAANEE-KSAATAEKNQTI

Parental  PGFHQAP
          PGF..AP
Retrocopy PGFQRAP

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	8.61 RPM
SRP051959_heart	0.02 RPM	7.84 RPM
SRP051959_kidney	0.02 RPM	8.28 RPM
SRP051959_liver	0.02 RPM	7.43 RPM
SRP051959_lung	0.02 RPM	6.98 RPM
SRP051959_lymph_node	0.00 RPM	7.74 RPM
SRP051959_skeletal_muscle	0.04 RPM	16.18 RPM
SRP051959_spleen	0.02 RPM	5.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_490 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_490 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_490 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016613	1 retrocopy	retro_cjac_490 ,
Oryctolagus cuniculus	ENSOCUG00000021569	1 retrocopy	retro_ocun_812,