RetrogeneDB ID: retro_cjac_148

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:74118712..74119090(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022603
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000008026
• Aliases: None
• Description: None

Sequence

>retro_cjac_148
ATGCTGTCCCACCTGCTGAAAGAACACCAGGCCAAACAGAATGAACACAAGGAGCTGCAGGAGAAGAGGAGGCGAGAAGC
TATCACAGCAGCGACCTGCCTGACAGAAGCTTTGGTGGATCACCTCAATGTGGGTGTAGCCCAGGCCTACATGAACCAGA
GAAAGCTGGACCATGAGGTGAAGACCCTACAGGTGCAGGCTGCCCAATTTGCCAAGCAGACAGGCCAGTGGATTGGAATG
GTGGAGAACTTCAACCAAGCACTCAAGGAAATTGGGGATGTGGAGAACTGGGCTCGGAGCATCGAGCTGGACATGCGCAC
CATTGCCACTGCACTGGAATATGTCTACGAAGGGCAGCTGCAGTCCGCCCCTTCCTAG

Alignment

ORF - retro_cjac_148 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLSRLLKEHQAKQNERKELQEKRRREAITAATCLTEALVDHLNVGVAQAYMNQRKLDHEVKTLQVQAAQF
          MLS.LLKEHQAKQNE.KELQEKRRREAITAATCLTEALVDHLNVGVAQAYMNQRKLDHEVKTLQVQAAQF
Retrocopy MLSHLLKEHQAKQNEHKELQEKRRREAITAATCLTEALVDHLNVGVAQAYMNQRKLDHEVKTLQVQAAQF

Parental  AKQTGQWIGMVENFNQALKENGDVENWARSIELDMRTIATALEYVYKGQLQSAPS
          AKQTGQWIGMVENFNQALKE.GDVENWARSIELDMRTIATALEYVY.GQLQSAPS
Retrocopy AKQTGQWIGMVENFNQALKEIGDVENWARSIELDMRTIATALEYVYEGQLQSAPS

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	2.20 RPM	7.48 RPM
SRP051959_heart	3.72 RPM	13.17 RPM
SRP051959_kidney	4.33 RPM	14.80 RPM
SRP051959_liver	3.62 RPM	12.89 RPM
SRP051959_lung	2.39 RPM	8.64 RPM
SRP051959_lymph_node	1.55 RPM	5.07 RPM
SRP051959_skeletal_muscle	13.21 RPM	39.13 RPM
SRP051959_spleen	2.04 RPM	8.45 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_148 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_148 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_148 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011918	1 retrocopy	retro_btau_878,
Canis familiaris	ENSCAFG00000000061	1 retrocopy	retro_cfam_1156,
Callithrix jacchus	ENSCJAG00000008026	1 retrocopy	retro_cjac_148 ,
Cavia porcellus	ENSCPOG00000001818	2 retrocopies	retro_cpor_1260, retro_cpor_846,
Macropus eugenii	ENSMEUG00000001570	3 retrocopies	retro_meug_12, retro_meug_1307, retro_meug_242,
Mus musculus	ENSMUSG00000090247	1 retrocopy	retro_mmus_1761,
Oryctolagus cuniculus	ENSOCUG00000010114	1 retrocopy	retro_ocun_1023,
Otolemur garnettii	ENSOGAG00000010506	1 retrocopy	retro_ogar_786,
Pteropus vampyrus	ENSPVAG00000017748	1 retrocopy	retro_pvam_121,
Sus scrofa	ENSSSCG00000000359	1 retrocopy	retro_sscr_850,
Ictidomys tridecemlineatus	ENSSTOG00000010338	1 retrocopy	retro_itri_467,