RetrogeneDB ID: retro_cjac_3824

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284793.1:1..1119(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011011
• Aliases: None
• Description: None

Sequence

>retro_cjac_3824
GCTGAGGAACGTATTGGAAATGTAAGAACTGTTCGAGCTTTTGGGAAAGAAATGACTGAAATAGAGAAATATGCCAGCAA
AGTGGACTATGTGATGCAGTTAGCAAGGAAAGAGGCATTCGCTCGGGCTGGCTTCTTTGGAGCGACTGGGCTGTCTGGAA
ACCTGATCGTGCTTTCTGTCCTGTACAAAGGAGGGCTGCTGATGGGTAGTGCCCGCATGACAGTGGGTGAACTCTCTTCC
TTCCTAATGTATGCTTTCTGGGTTGGAGTAAGCATTGGAGGTCTGAGCTCTTTTTACTAGGAGGTGATGAAAGGACTGGG
CGCCGGGGAGCGCCTCTGGGAGCTCCTGGAGAGAGAGAGACCAAGTTGCCTTTTAACGAGGGGGTCATCTTAAATGAGAA
AAGCTTCCAGGGTGCTTTGGAGTTTGAGAACATGCATTTTACCTATCCGGGTCACCCAGACGTGCCCATGTTTCAGGATT
TCAGCCTTTCCATTCCATCAGGATCTGTCACGGCAGTGGTTGGCCCAAGTGGTTCTGGCAAATCAACAGTGCTTTCGCTC
CTGCTGAGGTTGTATGACCGTGTGTCCGGAACTATGAGTCTTGATGGCCATGACATCCGTCAGCTAAACCCAGTGTGGCT
GAGATCCAAGATGGGACAGTGAGTCAGGAACCCATTTTTTTTTCTTGCTCTATCGCTGAGAACATTGCTTATGGCACTGA
CAACCCTTCCTCTGTGACTGCTGAGCAAGTCCAGAGAGTGGCTGAAGTGGCCAATGCAGTGGCCTTCATCCAGAACTTCC
CCCAAGGGCTCAACACTGTGGTTGGAGAAAAGGGTGTTCTCCTTTCAGGTGGGCAGAAACAGCAGATTGCAATTGCCCGT
GCTCTGCTTAAGAATCCCAAAATTATTCTCCTAGATGAAGCAACCAGTGTGCTGGATGCTGAAAATGAGTACCTTGTTCA
AGAAGCTCTAGATCGACTGATGGATGGAAGAACAGTGTTAATTATTGCCCATCGTCTCTCCACCATTAAGAATGCTAATA
CGGTTGCTGTTCTTGACCAAGGAAAAATTACGTGAATATGGAAAGCATGAAGAACTGCTTTCAAAACCAAATGGGATA

Alignment

ORF - retro_cjac_3824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.49 %
• Parental protein coverage: 50.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AEERIGNVRTVRAFGKEMTEIEKYASKVDYVMQLARKEAFARAGFFGATGLSGNLIVLSVLYKGGLLMGS
          AEERIGNVRTVRAFGKEMTEIEKYASKVDYVMQLARKEAFARAGFFGATGLSGNLIVLSVLYKGGLLMGS
Retrocopy AEERIGNVRTVRAFGKEMTEIEKYASKVDYVMQLARKEAFARAGFFGATGLSGNLIVLSVLYKGGLLMGS

Parental  AHMTVGELSSFLMYAFWVGVSIGGLSSFYSELMKGLGAGGRLWELLERE-PKLPFNEG-VILNEKSFQGA
          A.MTVGELSSFLMYAFWVGVSIGGLSSFY.E.MKGLGAG.RLWELLERE.P......G.VILNEKSFQGA
Retrocopy ARMTVGELSSFLMYAFWVGVSIGGLSSFY*EVMKGLGAGERLWELLERERPSCLLTRG<VILNEKSFQGA

Parental  LEFKNVHFTYPARPDVPIFQDFSLSIPSGSVTALVGPSGSGKSTVLSLLLRLYDPVSGTISLDGHDIRQL
          LEF.N.HFTYP..PDVP.FQDFSLSIPSGSVTA.VGPSGSGKSTVLSLLLRLYD.VSGT.SLDGHDIRQL
Retrocopy LEFENMHFTYPGHPDVPMFQDFSLSIPSGSVTAVVGPSGSGKSTVLSLLLRLYDRVSGTMSLDGHDIRQL

Parental  NPVWLRSKI-GTVSQEPILFSCSIAENIAYGADNPSSVTAEQVQRVAEVANAVAFIRNFPQGFNTVVGEK
          NPVWLRSK..GTVSQEPI.FSCSIAENIAYG.DNPSSVTAEQVQRVAEVANAVAFI.NFPQG.NTVVGEK
Retrocopy NPVWLRSKM<GTVSQEPIFFSCSIAENIAYGTDNPSSVTAEQVQRVAEVANAVAFIQNFPQGLNTVVGEK

Parental  GVLLSGGQKQRIAIARALLKNPKILLLDEATSALDAENEFLVQEALDRLMDGRTVLIIAHRLSTIKNANV
          GVLLSGGQKQ.IAIARALLKNPKI.LLDEATS.LDAENE.LVQEALDRLMDGRTVLIIAHRLSTIKNAN.
Retrocopy GVLLSGGQKQQIAIARALLKNPKIILLDEATSVLDAENEYLVQEALDRLMDGRTVLIIAHRLSTIKNANT

Parental  VAVLDQGKIT-EYGKHEELLSKPNGI
          VAVLDQGKIT.EYGKHEELLSKPNGI
Retrocopy VAVLDQGKIT>EYGKHEELLSKPNGI

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	10.69 RPM
SRP051959_heart	0.02 RPM	21.87 RPM
SRP051959_kidney	0.02 RPM	21.08 RPM
SRP051959_liver	0.02 RPM	13.82 RPM
SRP051959_lung	0.02 RPM	12.88 RPM
SRP051959_lymph_node	0.07 RPM	12.40 RPM
SRP051959_skeletal_muscle	0.02 RPM	13.19 RPM
SRP051959_spleen	0.08 RPM	24.62 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3824 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3824 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3824 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011011	1 retrocopy	retro_cjac_3824 ,
Dasypus novemcinctus	ENSDNOG00000023785	1 retrocopy	retro_dnov_2360,
Homo sapiens	ENSG00000135776	3 retrocopies	retro_hsap_1470, retro_hsap_1537, retro_hsap_1542,