RetrogeneDB ID: retro_cjac_75

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:124148172..124149018(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022751
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000009230
• Aliases: None
• Description: None

Sequence

>retro_cjac_75
AGTGGCGGCAGCGGCGGCGACGGCAGTAACGGCGGCGGCTACAGCGGGGACGCGAGCGGGGCGGTGACGGTGTGGGAGGT
GGTCTCACTCTTGGGGAAACTACTGGGCACCGTCGCCACGCTGAAGGTGATTCTGTACCTGCTCCGAGTGTGCTTAGCGA
TGGCCTGGAAATCCGGCGGCGCCAGCCACTCGGAGCTAATCCACAATCTCCGCAAAAATGGAATCATCAAGACAGATAAA
GTATTTGAAGTGATGCTGGCTACAGACCGCTCCCACTATGCAAAATGTAACCCTTACATGGATTCTCCACAATCAATAGG
TTTCCAAGCAACAATCAGTGCTCCACACATGCATGCATACGCACTAGAACTTCTGTTTGATCAATTGCATGAAGGAGCTA
AAGCTCTTGATGTAGGATCTGGAAGTGGAATCCTTACTGCATGTTTTGCACGTATGGTTGGATGTAGTGGAAAAGTCATA
GGAATTGATCACATTAAAGAGCTAGTAGATGACTCAATAAATAATGTCAGGAAGGATGATCCAACACCTCTGTCTTCAGG
GAGAGTACAACTTGTTGTGGGAGATGGAAGAATGGGGTATGCTGAAGAAGCCCCTTACGATGCCATTCACGTAGGAGCTG
CAGCCCCTGTTGTACCCCAGGCGCTAATAGACCAGTTAAAGCCTGGTGGAAGATTGATATTGCCAGTTGGTCCTGCAGGT
GGAAACCAAATGTTGGAGCAGTATGACAAGCTACAAGATGGCAGCGTCAAAATGAAGCCTCTGATGGGGGTGATATACGT
GCCTTTAACAGATAAAGAAAAGCAGTGGTCCAGGGATGAATTGTAA

Alignment

ORF - retro_cjac_75 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.28 %
• Parental protein coverage: 97.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGGSGGDGSNGGGYSGDASGAVTVWEVVSLLGKLLGTVAALKVILYLLRVCLAMAWKSGGASHSELIHNL
          SGGSGGDGSNGGGYSGDASGAVTVWEVVSLLGKLLGTVA.LKVILYLLRVCLAMAWKSGGASHSELIHNL
Retrocopy SGGSGGDGSNGGGYSGDASGAVTVWEVVSLLGKLLGTVATLKVILYLLRVCLAMAWKSGGASHSELIHNL

Parental  RKNGIIKTDKVFEVMLATDRSHYAKCNPYMDSPQSIGFQATISAPHMHAYALELLFDQLHEGAKALDVGS
          RKNGIIKTDKVFEVMLATDRSHYAKCNPYMDSPQSIGFQATISAPHMHAYALELLFDQLHEGAKALDVGS
Retrocopy RKNGIIKTDKVFEVMLATDRSHYAKCNPYMDSPQSIGFQATISAPHMHAYALELLFDQLHEGAKALDVGS

Parental  GSGILTACFARMVGCSGKVIGIDHIKELVDDSINNVRKDDPTLLSSGRVQLVVGDGRMGYAEEAPYDAIH
          GSGILTACFARMVGCSGKVIGIDHIKELVDDSINNVRKDDPT.LSSGRVQLVVGDGRMGYAEEAPYDAIH
Retrocopy GSGILTACFARMVGCSGKVIGIDHIKELVDDSINNVRKDDPTPLSSGRVQLVVGDGRMGYAEEAPYDAIH

Parental  VGAAAPVVPQALIDQLKPGGRLILPVGPAGGNQMLEQYDKLQDGSVKMKPLMGVIYVPLTDKEKQWSR
          VGAAAPVVPQALIDQLKPGGRLILPVGPAGGNQMLEQYDKLQDGSVKMKPLMGVIYVPLTDKEKQWSR
Retrocopy VGAAAPVVPQALIDQLKPGGRLILPVGPAGGNQMLEQYDKLQDGSVKMKPLMGVIYVPLTDKEKQWSR

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	0.42 RPM	9.83 RPM
SRP051959_heart	0.56 RPM	17.03 RPM
SRP051959_kidney	0.78 RPM	11.34 RPM
SRP051959_liver	0.93 RPM	9.68 RPM
SRP051959_lung	0.57 RPM	12.02 RPM
SRP051959_lymph_node	0.80 RPM	11.73 RPM
SRP051959_skeletal_muscle	0.20 RPM	19.83 RPM
SRP051959_spleen	0.67 RPM	11.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_75 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_75 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_75 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009230	1 retrocopy	retro_cjac_75 ,
Macaca mulatta	ENSMMUG00000029462	1 retrocopy	retro_mmul_134,
Oryctolagus cuniculus	ENSOCUG00000000499	2 retrocopies	retro_ocun_871, retro_ocun_955,
Ochotona princeps	ENSOPRG00000002833	2 retrocopies	retro_opri_171, retro_opri_434,
Tupaia belangeri	ENSTBEG00000000451	1 retrocopy	retro_tbel_883,