RetrogeneDB ID: retro_cjac_2710

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:31292263..31292971(+)
• Located in intron of: ENSCJAG00000010743

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYCP3
• Ensembl ID: ENSCJAG00000001658
• Aliases: None
• Description: synaptonemal complex protein 3 [Source:HGNC Symbol;Acc:18130]

Sequence

>retro_cjac_2710
ATGGTGTCCTCCGGAAAAAAGTATTCCAGGAAATCTGGGAAGCCAACCATGGAAGATCAGTTTACCAGAGCCTATGACTT
TGAGACTGAAGAAAAGAAAGATCCGAGTGGTTCAGAGGAAGATGTTACTGAAGGGAAGACTACAGTCATTGAGAAACCTA
GGAAGAAAAGATCTTCTGCAGGAGTAGTTGAAGATATGGGGTGTGAAGTACAGAATATGCTGGAAGGAGTTGGAGTTGAC
ATTAACAAGGCTCTTCTTGCCAAGAGAAAGAGACTAGAAATGTATACCAAGGCTTCTCTCAAAACTAGCAACCAGAAAAT
CGAACATGTTTGGAAAACACAACAAGATCAAAGGCAGAAACTTAACCAAAAATATTCTCAGCAGTTTCTGACTTTATTCC
AGCAATGGGATTTAGATATGCAGAAAGCTGAAGAACAAGAAGAAAAAATACTTAATATGTTTCGACAGCAACAAAAGATT
CTTCAACAATCTAGAATTGTTCAGAGCCAGAGACTGAAAACAATTAGACAGTTATATGAGCAGTTCATAAAGAGTATGGA
AGAGTTGGAGAAGAATCATGATAATCTACTTACTGGTGCACAAAATGAATTTAAAAAAGAAATGGCTATGTTGCAGAAAA
AAATTATGATGGAAACTCAGCAGCAAGAGATAGCATGTGTTCGGAAGTCTCTTCAATCCATGTTATTC

Alignment

ORF - retro_cjac_2710 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSSGKKYSRKSGKPSMEDQFTRAYDFETEEKKDPSGSEEDVTEGKTTVIEKPRKKRSSAGVVEDMGCEV
          MVSSGKKYSRKSGKP.MEDQFTRAYDFETEEKKDPSGSEEDVTEGKTTVIEKPRKKRSSAGVVEDMGCEV
Retrocopy MVSSGKKYSRKSGKPTMEDQFTRAYDFETEEKKDPSGSEEDVTEGKTTVIEKPRKKRSSAGVVEDMGCEV

Parental  QNMLEGVGVDINKALLAKRKRLEMYTKASLKTSNQKIEHVWKTQQDQRQKLNQEYSQQFLTLFQQWDLDM
          QNMLEGVGVDINKALLAKRKRLEMYTKASLKTSNQKIEHVWKTQQDQRQKLNQ.YSQQFLTLFQQWDLDM
Retrocopy QNMLEGVGVDINKALLAKRKRLEMYTKASLKTSNQKIEHVWKTQQDQRQKLNQKYSQQFLTLFQQWDLDM

Parental  QKAEEQEEKILNMFRQQQKILQQSRIVQSQRLKTIRQLYEQFIKSMEELEKNHDNLLTGAQNEFKKEMAM
          QKAEEQEEKILNMFRQQQKILQQSRIVQSQRLKTIRQLYEQFIKSMEELEKNHDNLLTGAQNEFKKEMAM
Retrocopy QKAEEQEEKILNMFRQQQKILQQSRIVQSQRLKTIRQLYEQFIKSMEELEKNHDNLLTGAQNEFKKEMAM

Parental  LQKKIMMETQQQEIACVRKSLQSMLF
          LQKKIMMETQQQEIACVRKSLQSMLF
Retrocopy LQKKIMMETQQQEIACVRKSLQSMLF

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	1.46 RPM
SRP051959_heart	0.02 RPM	1.12 RPM
SRP051959_kidney	0.00 RPM	1.44 RPM
SRP051959_liver	0.04 RPM	1.00 RPM
SRP051959_lung	0.02 RPM	0.91 RPM
SRP051959_lymph_node	0.07 RPM	0.84 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.28 RPM
SRP051959_spleen	0.00 RPM	1.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2710 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2710 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2710 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013389	2 retrocopies	retro_chof_1384, retro_chof_2693,
Callithrix jacchus	ENSCJAG00000001658	1 retrocopy	retro_cjac_2710 ,
Cavia porcellus	ENSCPOG00000001202	1 retrocopy	retro_cpor_686,
Dasypus novemcinctus	ENSDNOG00000017387	2 retrocopies	retro_dnov_2623, retro_dnov_739,
Dasypus novemcinctus	ENSDNOG00000017624	3 retrocopies	retro_dnov_2294, retro_dnov_2402, retro_dnov_420,
Echinops telfairi	ENSETEG00000007664	1 retrocopy	retro_etel_1510,
Myotis lucifugus	ENSMLUG00000010711	2 retrocopies	retro_mluc_1098, retro_mluc_1839,
Mus musculus	ENSMUSG00000067764	1 retrocopy	retro_mmus_1085,
Mus musculus	ENSMUSG00000072479	1 retrocopy	retro_mmus_1782,
Otolemur garnettii	ENSOGAG00000024543	1 retrocopy	retro_ogar_633,
Rattus norvegicus	ENSRNOG00000017224	1 retrocopy	retro_rnor_1728,
Ictidomys tridecemlineatus	ENSSTOG00000001853	1 retrocopy	retro_itri_931,