RetrogeneDB ID: retro_cjac_136

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:45675229..45675616(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000035652
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000008986
• Aliases: None
• Description: None

Sequence

>retro_cjac_136
ATGGCGGCCTCTGTACTGGGTTCGGTGCTGCGGACGTTCAAGCAGATGGTTCCTTCATCAGCTTCAGGCCAAGTTCGAGG
TTACTATGTAGACTGGAGAATGTGGCGTGATGTGAAGAGACGAAAAATGGCCTATGAATACGCAGATGAGAGACTACGTG
TTAATTCACTCAGGAAGAATACCATTTTGCCAAAACTTCTACAGGACGTAGCTGATGAAGAAATTGCTGCCTTCCCCCGG
GATAGCTGTCCCGTTAGAATCAGAAATCGGTGTGTTATGACGTCCCGTCCGCGTGGTGTGAAGCGGCGCTGGAGGCTTAG
TCGTACCGTCTTCCGTCACTTAGCAGACCATGGACAACTTTCTGGGGTCCAGCGAGCGATGTGGTAA

Alignment

ORF - retro_cjac_136 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASVLGSVLRTFKQMVPSSASGQVRGYYVDWRMWRDVKRRKMAYEYADERLRVNSLRKNTILPKLLQDV
          MAASVLGSVLRTFKQMVPSSASGQVRGYYVDWRMWRDVKRRKMAYEYADERLRVNSLRKNTILPKLLQDV
Retrocopy MAASVLGSVLRTFKQMVPSSASGQVRGYYVDWRMWRDVKRRKMAYEYADERLRVNSLRKNTILPKLLQDV

Parental  ADEEIAAFPRDSCPVRIRNRCVMTSRPRGVKRRWRLSRIVFRHLADHGQLSGVQRAMW
          ADEEIAAFPRDSCPVRIRNRCVMTSRPRGVKRRWRLSR.VFRHLADHGQLSGVQRAMW
Retrocopy ADEEIAAFPRDSCPVRIRNRCVMTSRPRGVKRRWRLSRTVFRHLADHGQLSGVQRAMW

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	0.04 RPM	2.73 RPM
SRP051959_heart	0.00 RPM	3.98 RPM
SRP051959_kidney	0.04 RPM	2.66 RPM
SRP051959_liver	0.09 RPM	5.20 RPM
SRP051959_lung	0.03 RPM	2.64 RPM
SRP051959_lymph_node	0.09 RPM	2.40 RPM
SRP051959_skeletal_muscle	0.02 RPM	4.43 RPM
SRP051959_spleen	0.04 RPM	3.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_136 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_136 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001109	1 retrocopy	retro_btau_149,
Callithrix jacchus	ENSCJAG00000008986	1 retrocopy	retro_cjac_136 ,
Mus musculus	ENSMUSG00000058267	1 retrocopy	retro_mmus_463,
Oryctolagus cuniculus	ENSOCUG00000026497	1 retrocopy	retro_ocun_34,
Tupaia belangeri	ENSTBEG00000003335	1 retrocopy	retro_tbel_1199,