RetrogeneDB ID: retro_cjac_277

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:2169589..2170234(+)
• Located in intron of: ENSCJAG00000021486

Retrocopy information

• Ensembl ID: ENSCJAG00000035055
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPL10
• Ensembl ID: ENSCJAG00000011822
• Aliases: None
• Description: None

Sequence

>retro_cjac_277
ATGGGCAGCCGCCCCGCCCGTTGTTACCAATATTGTAAGAACAAGCCGTACCCAAAGTCCCGCTTCTGCCGAGGTGTCCC
TGACGCCAAGATTCGCATCTTTGACCTGGGGCGGAAGAAGGCAAAAGTGGATGAGTTTCCACTCTGTGGCCACATGGTAT
CGGATGAATATGAGCAGCTCTCCTCTGGAGCCCTGGAGGCTGCCCGAATTTGTGCCAATAAGTACACGGTGAAAAGTTGT
GGCAAAGATGGCTTTCATATCCGAGTGCGGCTCCATCCCTTCCACGTCATCCGCATCAACAAGATGTTGTCCTGTGCTGG
GGCTGACAGGCTCCAAACAGGCATGCGAGGCGCCTTTGGAAAGCCCCAGGGCACTGTGGCCAGGGTTCACATTGGCCAAG
TGATCACGTCCATCCGCGCCAAGCTGCAGAACAAGGAGCATGTGATTGAGGCCCTGCGCAGGGCCAAGTTCAAGTTCCCT
GGCCACCAGAAGATCCACATCTCAAAGAAGTGGGGCTTCACCAAGTTCAGTGCCGATGAATTTGAAGACATGGTGGCTGA
GAAGCAGCTCATCCCAGATGGCTGTGGGGTTAAGTACATCCCCAATCGTGGCCCTCTGGACAAGTGGCGGGCCCTGCACT
CATGA

Alignment

ORF - retro_cjac_277 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
          MG.RPARCY.YCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSS.ALEAARI
Retrocopy MGSRPARCYQYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSGALEAARI

Parental  CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRT
          CANKY.VKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVI.SIR.
Retrocopy CANKYTVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVITSIRA

Parental  KLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWR
          KLQNKEHVIEALRRAKFKFPG.QKIHISKKWGFTKF.ADEFEDMVAEK.LIPDGCGVKYIPNRGPLDKWR
Retrocopy KLQNKEHVIEALRRAKFKFPGHQKIHISKKWGFTKFSADEFEDMVAEKQLIPDGCGVKYIPNRGPLDKWR

Parental  ALHS
          ALHS
Retrocopy ALHS

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	0.13 RPM	224.20 RPM
SRP051959_heart	0.11 RPM	175.81 RPM
SRP051959_kidney	0.20 RPM	206.53 RPM
SRP051959_liver	0.32 RPM	287.35 RPM
SRP051959_lung	0.23 RPM	185.19 RPM
SRP051959_lymph_node	0.25 RPM	334.37 RPM
SRP051959_skeletal_muscle	0.20 RPM	304.88 RPM
SRP051959_spleen	0.19 RPM	320.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_277 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_277 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_277 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011822	5 retrocopies	retro_cjac_156, retro_cjac_174, retro_cjac_260, retro_cjac_277 , retro_cjac_61,
Felis catus	ENSFCAG00000011395	1 retrocopy	retro_fcat_81,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,
Oryctolagus cuniculus	ENSOCUG00000015919	2 retrocopies	retro_ocun_107, retro_ocun_147,
Rattus norvegicus	ENSRNOG00000027149	5 retrocopies	retro_rnor_1007, retro_rnor_1090, retro_rnor_270, retro_rnor_2998, retro_rnor_482,