RetrogeneDB ID: retro_cjac_3087

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:82082248..82083096(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000006503
• Aliases: None
• Description: None

Sequence

>retro_cjac_3087
ATGGAACACGGCTTCATCATCACCCAGGCGCGGAGGGAAGACGCCCTGGTGCTCACCAAGTAAGGCCTGGTCTCCAAATC
CTCTCCTAAGAAGCCTCTTGGACGTAACATCTTCAAGGCCCTTTTCTGCTGTTTTCGCGCCCAGCATGTTGGCCAGTCAA
GTTGCTCCACTGAGCTCGCTGCGTATAAGGAGGAAGTGAACACCATTGCTAAGTCGGATCTGCTCCAGTGTCTCCAGTAC
CAGTTCTACCAGATCCCAGGGACCTGCCTGCTCCCAGAGGTGACAGAGTAAGATCAAGGAAGGATCTGTGTGGTCATTGA
CCTGGACGAAACCCTGGTGCACAGCTCCTTTAAGCCAATCAACAATGCTGACTTCATAGTGCCTACAGAGATTGAGGGGA
CCACTCACCAGGTGTATGTGCTCAAGAGGCCTTATGTGGACGAGTTCCTGAGACGCATGGGGGAACTCTTTGAATGTGTT
CTCTTCACTGCCAGCCTGGCCAAGTATGCCGACCCTGTGACGGACCAGCTGGACTGGTGTGGGGTGTTCCAGGCCCGCCT
ATTCCGTGAGTCCTGCGTGTTTCACCAGGGATGCTACGTCAAGGACCTCGGCCGCCTGGGGAGGGACCTGAGGAAGACTC
TCATCCTGGACAACTCGCTTACTTCTTACATCTTCCACCCTGAGAATGTAGTTCCTGTGCAGTCTTGGTTTGATGACATG
GCAGACACCGAGTTGCTGAACCTGATCCCAATCTTTGAGGAGCTGAGCAGAGCAGAGGACGTCTACACCAGCCTTGGGCA
GCTGCGGGCCCCTTAGACTTCCCTGCTTCCAGGCAACGGCCATCCCAG

Alignment

ORF - retro_cjac_3087 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEHGSIITQARREDALVLTKQGLVSKSSPKKPRGRNIFKALFCCFRAQHVGQSSCSTELAAYKEEANTIA
          MEHG.IITQARREDALVLTK.GLVSKSSPKKP.GRNIFKALFCCFRAQHVGQSSCSTELAAYKEE.NTIA
Retrocopy MEHGFIITQARREDALVLTK*GLVSKSSPKKPLGRNIFKALFCCFRAQHVGQSSCSTELAAYKEEVNTIA

Parental  KSDLLQCLQYQFYQIPGTCLLPEVTEEDQGRICVVIDLDETLVHSSFKPINNADFIVPIEIEGTTHQVYV
          KSDLLQCLQYQFYQIPGTCLLPEVTE.DQGRICVVIDLDETLVHSSFKPINNADFIVP.EIEGTTHQVYV
Retrocopy KSDLLQCLQYQFYQIPGTCLLPEVTE*DQGRICVVIDLDETLVHSSFKPINNADFIVPTEIEGTTHQVYV

Parental  LKRPYVDEFLRRMGELFECVLFTASLAKYADPVTDLLDRCGVFRARLFRESCVFHQGCYVKDLSRLGRDL
          LKRPYVDEFLRRMGELFECVLFTASLAKYADPVTD.LD.CGVF.ARLFRESCVFHQGCYVKDL.RLGRDL
Retrocopy LKRPYVDEFLRRMGELFECVLFTASLAKYADPVTDQLDWCGVFQARLFRESCVFHQGCYVKDLGRLGRDL

Parental  RKTLILDNSPASYIFHPENAVPVQSWFDDMADTELLNLIPIFEELSGAEDVYTSLG-AAGPLA-FPASRR
          RKTLILDNS..SYIFHPEN.VPVQSWFDDMADTELL.................SLG...GPL..FPASR.
Retrocopy RKTLILDNSLTSYIFHPENVVPVQSWFDDMADTELLXXXXXXXXXXXXXXXXXSLG>SCGPLR>FPASRQ

Parental  WPSQ
          .PSQ
Retrocopy RPSQ

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	0.02 RPM	63.52 RPM
SRP051959_heart	0.07 RPM	62.07 RPM
SRP051959_kidney	0.07 RPM	48.96 RPM
SRP051959_liver	0.02 RPM	43.54 RPM
SRP051959_lung	0.07 RPM	76.15 RPM
SRP051959_lymph_node	0.07 RPM	49.70 RPM
SRP051959_skeletal_muscle	0.07 RPM	87.02 RPM
SRP051959_spleen	0.00 RPM	63.30 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3087 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3087 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3087 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005618	1 retrocopy	retro_chof_1918,
Callithrix jacchus	ENSCJAG00000002423	1 retrocopy	retro_cjac_4201,
Callithrix jacchus	ENSCJAG00000006503	2 retrocopies	retro_cjac_3087 , retro_cjac_919,
Homo sapiens	ENSG00000175215	2 retrocopies	retro_hsap_4315, retro_hsap_4319,
Macaca mulatta	ENSMMUG00000005321	2 retrocopies	retro_mmul_2208, retro_mmul_764,
Mus musculus	ENSMUSG00000078429	1 retrocopy	retro_mmus_612,
Nomascus leucogenys	ENSNLEG00000017164	2 retrocopies	retro_nleu_1741, retro_nleu_3079,
Petromyzon marinus	ENSPMAG00000009544	2 retrocopies	retro_pmar_20, retro_pmar_27,
Pongo abelii	ENSPPYG00000004711	14 retrocopies	retro_pabe_1708, retro_pabe_1739, retro_pabe_1740, retro_pabe_1742, retro_pabe_1746, retro_pabe_1762, retro_pabe_2402, retro_pabe_2592, retro_pabe_3202, retro_pabe_3205, retro_pabe_3221, retro_pabe_3237, retro_pabe_3554, retro_pabe_3578,
Pan troglodytes	ENSPTRG00000005155	7 retrocopies	retro_ptro_2587, retro_ptro_2589, retro_ptro_2590, retro_ptro_2592, retro_ptro_2594, retro_ptro_2958, retro_ptro_3054,