RetrogeneDB ID: retro_cjac_108

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:29475198..29475894(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033985
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000021584
• Aliases: None
• Description: None

Sequence

>retro_cjac_108
ATGGCTGGCTTGGTGGATTTCCAGAATGAGGAAGAGGTGAAGTCCTTTTTGGAGAACATGGAGGTGGAGTGCAACTACCA
TTGCTACCATGAGAAGGATCCGGACAGTTGCAATCGGCTGGTGGACTATTTGGAAGGGATCCAGAAGAATTTTGATGAGG
TTGCCAAGGTGTTGAAGTTTAACTGTGAAGACAACCAGCACAGCAATAGCTGCTACAAACTGGGGGCCTACTATGTGACT
GGAAAAGGTGGTCTGACCCAGGACCTGAAAGCTGCTGCCAGTTGCTTTTTGATAGTGTGTGAGAAGCCCAGAAAGAAGTC
TTTAGCAGCATGTCACAACGTTGCTTGCCTGGCACATGATGGATGGGTTAATGAGGATGGCCAGCCTGACCTGGGGAAGG
CCAGGGACTACTACATAAGGGCCTGTGATGCTGGTTATGCCTCCAGCTGCTTCAACCTCAGTGCCATGTTCCTGCAGGGT
GCCCCTGGCTTTCCCAAGGACATGGACCTGGAATGTAAATATTCCATGAAAGCCTGTGGCCTGGGTCATTTCTGGGCCTG
TGCCAATGCCAGTCACATGTACAAGCTGGGGGATGGCATCGAAAAGGATGAGGCCAAGGCTGAGGTGCTAAAAATTCAAG
CCAAGCAGTTACACAAAGAACGGCAGAAAAGTGTCCAATCCTTAACATTTGTGTAA

Alignment

ORF - retro_cjac_108 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.61 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGLVDFQNEEEVKSFLENMEVECNYHCYHEKDPDGCYRLVDYLEGIQKNFDEAAKVLKFNCEDNQHSDS
          MAGLVDFQNEEEVKSFLENMEVECNYHCYHEKDPD.C.RLVDYLEGIQKNFDE.AKVLKFNCEDNQHS.S
Retrocopy MAGLVDFQNEEEVKSFLENMEVECNYHCYHEKDPDSCNRLVDYLEGIQKNFDEVAKVLKFNCEDNQHSNS

Parental  CYKLGAYYVTGKGGLTQDLKAAASCFLIACEKPGKKSLAACHNVARLAHDGRVNEDGQPDLGKARDYYTR
          CYKLGAYYVTGKGGLTQDLKAAASCFLI.CEKP.KKSLAACHNVA.LAHDG.VNEDGQPDLGKARDYY.R
Retrocopy CYKLGAYYVTGKGGLTQDLKAAASCFLIVCEKPRKKSLAACHNVACLAHDGWVNEDGQPDLGKARDYYIR

Parental  ACDAGYASSCFNLSAMFLQGAPGFPKDMDLACKYSMKACDLGHFWACANASRMYKLGDGVEKDEAKAEVL
          ACDAGYASSCFNLSAMFLQGAPGFPKDMDL.CKYSMKAC.LGHFWACANAS.MYKLGDG.EKDEAKAEVL
Retrocopy ACDAGYASSCFNLSAMFLQGAPGFPKDMDLECKYSMKACGLGHFWACANASHMYKLGDGIEKDEAKAEVL

Parental  KNRAEQLHKEQQKSVQSLTF
          K..A.QLHKE.QKSVQSLTF
Retrocopy KIQAKQLHKERQKSVQSLTF

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	3.19 RPM
SRP051959_heart	0.00 RPM	3.60 RPM
SRP051959_kidney	1.22 RPM	4.57 RPM
SRP051959_liver	0.00 RPM	4.92 RPM
SRP051959_lung	0.00 RPM	3.35 RPM
SRP051959_lymph_node	0.00 RPM	4.06 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.45 RPM
SRP051959_spleen	0.00 RPM	3.93 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_108 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_108 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021584	1 retrocopy	retro_cjac_108 ,
Ictidomys tridecemlineatus	ENSSTOG00000008063	2 retrocopies	retro_itri_1126, retro_itri_1335,