RetrogeneDB ID: retro_cjac_2573

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:140852043..140853090(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000019391
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SHC1
• Ensembl ID: ENSCJAG00000009236
• Aliases: None
• Description: None

Sequence

>retro_cjac_2573
GCTGGAATGCCAGTCACTCTCACCATCTCCACCAGCAGTCTCAACCTCATGGCCACAGACTGCAAGCAGATCATCGCCAA
CCACCACGTGCAATCTATCTCATTTGCATCCGGCGGGGATCCGGACACAGCTGAGTATGTCGCCTATGTTGCCAAAGACC
CTGTGAATCAGAGAGCCTGCCACATTCTGGAGTGTCCTGAAGGGCTTGCCCAGGATGTTATCAGCACCATTGGCCAGGCC
TTCGAGTTGCGCTTCAAACAATACCTCAGGAACCCACCCAAACTGGTCCCCCCCCATGACAGGATGGCTGGCTTTGATGG
CTCAGCTTGGGATGAAGAGGAGGAAGAGCCACCTGACCATCAGCACTATGACTTCCCAAGGGAAGGAATCCCCTCTTGGG
GGGGTAGTAGACATGAGGCTTCAGGAAGGAGCCACTCTACTCGCTGCCCAGACCCCCAGCCACTTGGGAGCTACACTGCC
TATAGGACAGCCTGTTGGGGGAGATCCAGAAGTCCGCAAACAGATGCCACTTCCACCACCCTGTCCAGCAGGCGGAGAGC
CCTTTGATGATCCCTCCTACCGCAACGTCCAGAACCTAGACAAGGCCCAGCAAGCAGGGGGTGGTGCTGGGCCCCCCAAT
CCTGCCATCAATGGCAGCGTGCCCCAGGACCTATTTGACATGAAGCCCTTTGAAGATGTTCTTCGGGTGCCTCCACCTCC
CCAGTCGGTGACCATGGCTGAGCAGCTCCGAGGGGAGCCCTGGTTTCATGGGAAGCTGAGCCGGCGGGAGGCTGAGGCAC
TGCTGCAGCTCAATGGGACTTCCTGGTGCGGGAGAGCACGACCACACCTGGCCAGTATGTGCTCACTGGCTTGCAGAGTG
GGCAGCCCAAGCATCTGCTACTGATGGACCCTGAGGGTGTGGTATGGACAAAGGATCACCACTTTGAGAGTGTCAGTCAC
CTCATCAGCTACCACACGGACAATCACTTGCCCATCATCTCTGCGGGCAGCGAACTGTGTCTACAGCAACCTGTGGAGCG
GAAACTG

Alignment

ORF - retro_cjac_2573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.18 %
• Parental protein coverage: 60.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGMPITLTISTSSLNLMAADCKQIIANHHMQSISFASGGDPDTAEYVAYVAKDPVNQRACHILECPEGLA
          AGMP.TLTISTSSLNLMA.DCKQIIANHH.QSISFASGGDPDTAEYVAYVAKDPVNQRACHILECPEGLA
Retrocopy AGMPVTLTISTSSLNLMATDCKQIIANHHVQSISFASGGDPDTAEYVAYVAKDPVNQRACHILECPEGLA

Parental  QDVISTIGQAFELRFKQYLRNPPKLVTPHDRMAGFDGSAWDEEEEEPPDHQYYNDFP-GKEPPLGGVVDM
          QDVISTIGQAFELRFKQYLRNPPKLV.PHDRMAGFDGSAWDEEEEEPPDHQ.Y.DFP.GKE.PLGGVVDM
Retrocopy QDVISTIGQAFELRFKQYLRNPPKLVPPHDRMAGFDGSAWDEEEEEPPDHQHY-DFP>GKESPLGGVVDM

Parental  RLREGATPPTAQTPSHLGATLPIGQPVGGDPEVRKQMPLPPPCPAGRELFDDPSYVNVQNLDKARQAGGG
          RL.EGAT...AQTPSHLGATLPIGQPVGGDPEVRKQMPLPPPCPAG.E.FDDPSY.NVQNLDKA.QAGGG
Retrocopy RLQEGATLLAAQTPSHLGATLPIGQPVGGDPEVRKQMPLPPPCPAGGEPFDDPSYRNVQNLDKAQQAGGG

Parental  AGPPNPAINGSAPRDLFDMKPFEDALRVPPPPQSVTMAEQLRGEPWFHGKLSRREAEALLQLNG-DFLVR
          AGPPNPAINGS.P.DLFDMKPFED.LRVPPPPQSVTMAEQLRGEPWFHGKLSRREAEALLQLNG.DFLVR
Retrocopy AGPPNPAINGSVPQDLFDMKPFEDVLRVPPPPQSVTMAEQLRGEPWFHGKLSRREAEALLQLNG<DFLVR

Parental  ESTTTPGQYVLTGLQSGQPKHLLLVDPEGVVRTKDHRFESVSHLISYHMDNHLPIISAGSELCLQQPVER
          ESTTTPGQYVLTGLQSGQPKHLLL.DPEGVV.TKDH.FESVSHLISYH.DNHLPIISAGSELCLQQPVER
Retrocopy ESTTTPGQYVLTGLQSGQPKHLLLMDPEGVVWTKDHHFESVSHLISYHTDNHLPIISAGSELCLQQPVER

Parental  KL
          KL
Retrocopy KL

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	36.41 RPM
SRP051959_heart	0.00 RPM	30.15 RPM
SRP051959_kidney	0.00 RPM	34.10 RPM
SRP051959_liver	0.02 RPM	17.26 RPM
SRP051959_lung	0.00 RPM	27.59 RPM
SRP051959_lymph_node	0.05 RPM	33.42 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.48 RPM
SRP051959_spleen	0.00 RPM	28.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2573 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2573 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2573 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009236	1 retrocopy	retro_cjac_2573 ,
Homo sapiens	ENSG00000160691	1 retrocopy	retro_hsap_4690,
Nomascus leucogenys	ENSNLEG00000011515	1 retrocopy	retro_nleu_2362,
Pongo abelii	ENSPPYG00000000769	1 retrocopy	retro_pabe_3643,
Pan troglodytes	ENSPTRG00000001397	1 retrocopy	retro_ptro_3117,
Tarsius syrichta	ENSTSYG00000011380	1 retrocopy	retro_tsyr_1773,