RetrogeneDB ID: retro_cjac_3630

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01190418.1:5042..6479(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000003303
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COLEC12
• Ensembl ID: ENSCJAG00000000146
• Aliases: None
• Description: None

Sequence

>retro_cjac_3630
AGTCAACCAAAAGAAACTTGGGAGAATAACTTCCCTCATCACCACTGTAAACAAAACCCTCCAGGCGTACAATGGCTATG
TCACGAATCTGCAGCAAGATACCAGTGTGCTCCAGGGTAATCTGCAGAACCAAATGTATTCTCATAACGTGGTCATCATG
AACCTCAACAACCTGAACCTGACCCAGGTACAGCAGAGGAACCTCATCACGAATCTGCAGCAGTCTGTGGATGACACAAG
CCAGGCTATCCAGCAAATCAAGAATGACTTTCAAAATCTGCAGCAGGTTTTTCTTCAAGCCAAGAAGGACACAGATTGGC
TGAAGGAGGAAGTGCAAAGCTTGCAGATGCTGGCTACCAATAATTCTGCTTTGGCCAAAGCCAACAACAACACCCTGGAG
GATATGAACAGCCAGCTCAACTCATTTACAGGTCTGATGGAGAACATCACTATCTCTCAGGCCAACGAGCAGAACCTGAA
AGACCTGCAGAACTTACACAAGGATGCAGAGAATAGAATGGCCATCAGGTTCAACCAACTGGAGGAACACTTCCAGCTCT
TTGAGATGGATATTGTAAATATCATTAGCAATATCAGTTACACAGCCCACCACCTGCAGATGCTGACTAGCAATCTGAAT
GAAGTCAGGACCACTTGCATGGATACCCTAACCAAACACAAGGTTTATCTGGCCTCCTTGAATAATACCCTGGCCAATAT
CTGTTTGGATTCTGTTTCTCTCAGGATGCAACAAGATTTGATGAGAGTGAGATTAGACACTGAAGTAAGCAACTTATCAG
TGATTATGGAAGAAATGAAGCTAGTAGACTCCAAGCATGGTCAGCTCATCAAGAATTTTACAATACTGCAAGGTCCACCC
AGCCCCAGTGTCCAAAAGGTGACAGAGGATCCCAGGGACACCCTGGTCCAACTGGCAACAAAGGACAGAAAGGAGAGAAG
GGGGAACCTGGACCACCCGGCCCTGTGGGTGAGAGAGGCCCAATGGGACCAGTCGGTCCCCCTGGAGAGTGTGGCGGCAA
AGGCTCTAAAGGCTCCCAGGGACCCAAAGACTCCCGTGTTTTCCCCGGGAATCCCAGCCCCAGGGCCCCAGTGGGGAACC
AGGCTCCCCAGGCCCACTGTGCAAAGAAGGACTCCCTGGCCCCCATGGCCCTCCTAGCTTCCAGGGACTACGGGGCACCA
TGGGGGAGCCTGGGGTGCCTGGACCTAGGGGACTGCCAGATTTGCCTGGGGTACCAGGCATGCCAGGGCCCAAGGGTCTC
CCTGACCCCCCAGACCATCAGAGCAGTGGTTGCCCCTGACCCTGCAGAATGAGCCAACCCCTGCACCGGAGATAATGGCT
GCCTGCCTCACTGGAAGACTTCACAGACCATGCTACTATTTTTCGTTGAGATGAAATTTTTGAGGAATGCAAAGCTT

Alignment

ORF - retro_cjac_3630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.74 %
• Parental protein coverage: 65.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  SQLKETLENNSF-LITTVNKTLQAYNGYVTNLQQDTSVLQGNLQNQMYSHNVVIMNLNNLNLTQVQQRNL
          SQ.KET.E.N.F.LITTVNKTLQAYNGYVTNLQQDTSVLQGNLQNQMYSHNVVIMNLNNLNLTQVQQRNL
Retrocopy SQPKETWE-NNF>LITTVNKTLQAYNGYVTNLQQDTSVLQGNLQNQMYSHNVVIMNLNNLNLTQVQQRNL

Parental  ITNLQRSVDDTSQAIQRIKNDFQNLQQVFLQAKKDTDWLKEKVQSLQMLATNNSALAKANNDTLEDMNSQ
          ITNLQ.SVDDTSQAIQ.IKNDFQNLQQVFLQAKKDTDWLKE.VQSLQMLATNNSALAKANN.TLEDMNSQ
Retrocopy ITNLQQSVDDTSQAIQQIKNDFQNLQQVFLQAKKDTDWLKEEVQSLQMLATNNSALAKANNNTLEDMNSQ

Parental  LNSFTGQMENITTISQANEQNLKDLQDLHKDAENRTAIKFNQLEERFQLFETDIVNIISNISYTAHHLRT
          LNSFTG.MENI.TISQANEQNLKDLQ.LHKDAENR.AI.FNQLEE.FQLFE.DIVNIISNISYTAHHL..
Retrocopy LNSFTGLMENI-TISQANEQNLKDLQNLHKDAENRMAIRFNQLEEHFQLFEMDIVNIISNISYTAHHLQM

Parental  LTSNLNEVRTTCTDTLTKHTDDLTSLNNTLANIRLDSVSLRMQQDLMRSRLDTEVANLSVIMEEMKLVDS
          LTSNLNEVRTTC.DTLTKH...L.SLNNTLANI.LDSVSLRMQQDLMR.RLDTEV.NLSVIMEEMKLVDS
Retrocopy LTSNLNEVRTTCMDTLTKHKVYLASLNNTLANICLDSVSLRMQQDLMRVRLDTEVSNLSVIMEEMKLVDS

Parental  KHGQLIKNFTILQGPPG-PRGPKGDRGSQGPPGPTGNKGQKGEKGEPGPPGPAGERGPMGPVGPPGERGS
          KHGQLIKNFTILQGPP..P..PKGDRGSQG.PGPTGNKGQKGEKGEPGPPGP.GERGPMGPVGPPGE.G.
Retrocopy KHGQLIKNFTILQGPPS<PQCPKGDRGSQGHPGPTGNKGQKGEKGEPGPPGPVGERGPMGPVGPPGECGG

Parental  KGSKGSQGPKGSRGSPGKPG-PQGPSGDPGPPGPPGKEGLPGPHGPPGFQGLQGTVGEPGVPGPRGLPGL
          KGSKGSQGPK.SR..PG.P..PQGPSG.PG.PGP..KEGLPGPHGPP.FQGL.GT.GEPGVPGPRGLP.L
Retrocopy KGSKGSQGPKDSRVFPGNPS<PQGPSGEPGSPGPLCKEGLPGPHGPPSFQGLRGTMGEPGVPGPRGLPDL

Parental  PGVPGMPGPKGPPGPPG-PSGAVVPLALQNEPTPAPE-DNGCPPHWK-NFTD-KCYYFS-VEKEIFEDAK
          PGVPGMPGPKG.P.PP..PS....PL.LQNEPTPAPE.DNGC.PHWK..FTD..CYYFS.VE......AK
Retrocopy PGVPGMPGPKGLPDPPD<PSEQWLPLTLQNEPTPAPE<DNGCLPHWK<DFTD<PCYYFS<VEMKFLRNAK

Parental  L
          L
Retrocopy L

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	0.00 RPM	10.45 RPM
SRP051959_heart	0.00 RPM	26.56 RPM
SRP051959_kidney	0.00 RPM	10.56 RPM
SRP051959_liver	0.00 RPM	1.47 RPM
SRP051959_lung	0.00 RPM	50.27 RPM
SRP051959_lymph_node	0.00 RPM	6.58 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.75 RPM
SRP051959_spleen	0.00 RPM	5.38 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3630 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3630 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3630 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000146	4 retrocopies	retro_cjac_3363, retro_cjac_3473, retro_cjac_3628, retro_cjac_3630 ,
Otolemur garnettii	ENSOGAG00000003364	1 retrocopy	retro_ogar_2320,