RetrogeneDB ID: retro_cjac_3363

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01174997.1:26932..28703(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000013841
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_3363
AGTCAACTAAAAGAAACTTGGGAGAATAACTTCCCTCATCACCACTGTAAACAAAACCCTCCAGGTGTACAATGGCTATG
TCATGAATCTGCAGCAAGATACCAGTGTGCTCCAGGGTAATCTGCAGAACCAAATGTATTCTCATAACGTGGTCATCATG
AACCTCAACAGCCTGAACCTGACCCAGGTACAGCAGAGGAACCTCATCACGAATCTGCAGTGGTCTGTGGATGACACAAG
CCAGTCTATCCAGCAAATCAAGAATGACTTTCAAAATCTGCAGCAGGTTTTTCTTCAAGCCAAGAAGGACACAGATTGGC
TGAAGGAGAAAGTGCAAAGCTTGCAGATGCTAGCTACCAATAATTCTGCTTTGGCCAAAGCTGACAAGGACACCCTGGAG
GATATGAACAGCCAGCTCAACTCATTTACAGGTCAGATGGAGAACATCACTATCTCTCAGGCCAACGAGCAGAACCTGAA
AGACCTGCAGAACTTACACAAGGATGCAGAGAATAGAACGGCCATCAGGTTCAACCAACTGGAGGAACACTTCCAACTCT
TTGAGACGGAAATTGTAAATATCATTAGCAATATCAGTTACACAGCCCACCACCTGCGGATGCTGACTAGCAATCTGAAT
GAAGTCAGAACCACTTGCATGGATACCCTAACCAAACACAACAAGGATGATCTGACCTCCTTGAATAATACCCTGGCCAA
CATCTGTTTGGATTCTGTTTCTCTCAGGATGCAACAAGATTTGATGAGATTGAGGTTAGACACTGAAGTAAGCAACTTAT
CAGTGATTATGGAAGAAATGAAGCTAGTAGACTCCAAGCATGGTCAGCTCATCAAGAATTTTACAGTACTGCAAGGTCCA
CCCAGCCCCAGTGTCCAAAAGGTGACAGAGGATCCCAGGGACTCCCTGGTCCAACTGGCAACAAGGGACAGAAAGGAGAG
AAGGGGGAACCTGGACCGCCCGGCCCTGTGGGTGAGAGAGGCCCAATGGGACCAGTCGGTCCCCCTGGAGAGTGTGGCAG
CAAAGGCTCTAAAGGCTCCCAGGGACCCAAAGACTCCCATGGTTCCCCCGGGAAGCCCGGCCCCCAGGGCCCCAGTGGGG
ACCCAGGCCCCCCAGGCCCACTGTGCAAAGAAGGACTCCCTGGCCCCCATAGCCCTCCTGGCTTCCAGGGACTACAGGGC
ACCATGGGGGAGCCTGGGGTGCCTGGACCTTGGGGACTGCCAGGTTTGCCTGGGGTACCAGGCATGCCAGGACCCAAGGG
TCCCCCGACCCCCCAGCCCATCAGGAGCAGTGGTGCCCCTGGCCCTGCAGAATGAGCCCACCCCTGCACCAGAGGACAAT
GGCTGCCCGCCTCACTGGAAGAACTTCACAGACAAATGCTACTATTTTTCCATTGAGAAAGAAATTTTTGAGGATGCAAA
GCTTTTCTGTGAAGACAAGTCTTCACATCTCGTTTTCATAAACACTAGAGAAGAACAGCAATGGATTAAAAAACAGATGG
TAGGGAGACAGAGCCACTGGATTGGCCTCACAGACTCAGAGAATGAAAATGAATGGAAGTGGCTGGATGGGACATTTCCA
GACTACAAAAGTTGGAAAGCTGGACAGCCGGATAACTGGGGTCATGGCCGCGGGTCAGGAGAAGACTGTGCTGGGTTGAT
TTATGCTGGGCAGTGGAACGATTTCCAGTGTGAAGACATCAATAACTTCATTTGTGAAAAAGACAGGGAGACAGTATTGT
CATCTGTATTA

Alignment

ORF - retro_cjac_3363 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.27 %
• Parental protein coverage: 79.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SQLKETLENNSF-LITTVNKTLQAYNGYVTNLQQDTSVLQGNLQNQMYSHNVVIMNLNNLNLTQVQQRNL
          SQLKET.E.N.F.LITTVNKTLQ.YNGYV.NLQQDTSVLQGNLQNQMYSHNVVIMNLN.LNLTQVQQRNL
Retrocopy SQLKETWE-NNF>LITTVNKTLQVYNGYVMNLQQDTSVLQGNLQNQMYSHNVVIMNLNSLNLTQVQQRNL

Parental  ITNLQRSVDDTSQAIQRIKNDFQNLQQVFLQAKKDTDWLKEKVQSLQMLATNNSALAKANNDTLEDMNSQ
          ITNLQ.SVDDTSQ.IQ.IKNDFQNLQQVFLQAKKDTDWLKEKVQSLQMLATNNSALAKA..DTLEDMNSQ
Retrocopy ITNLQWSVDDTSQSIQQIKNDFQNLQQVFLQAKKDTDWLKEKVQSLQMLATNNSALAKADKDTLEDMNSQ

Parental  LNSFTGQMENITTISQANEQNLKDLQDLHKDAENRTAIKFNQLEERFQLFETDIVNIISNISYTAHHLRT
          LNSFTGQMENIT.ISQANEQNLKDLQ.LHKDAENRTAI.FNQLEE.FQLFET.IVNIISNISYTAHHLR.
Retrocopy LNSFTGQMENIT-ISQANEQNLKDLQNLHKDAENRTAIRFNQLEEHFQLFETEIVNIISNISYTAHHLRM

Parental  LTSNLNEVRTTCTDTLTKHT-DDLTSLNNTLANIRLDSVSLRMQQDLMRSRLDTEVANLSVIMEEMKLVD
          LTSNLNEVRTTC.DTLTKH..DDLTSLNNTLANI.LDSVSLRMQQDLMR.RLDTEV.NLSVIMEEMKLVD
Retrocopy LTSNLNEVRTTCMDTLTKHNKDDLTSLNNTLANICLDSVSLRMQQDLMRLRLDTEVSNLSVIMEEMKLVD

Parental  SKHGQLIKNFTILQGPPGP-RGPKGDRGSQGPPGPTGNKGQKGEKGEPGPPGPAGERGPMGPVGPPGERG
          SKHGQLIKNFT.LQGPP.P...PKGDRGSQG.PGPTGNKGQKGEKGEPGPPGP.GERGPMGPVGPPGE.G
Retrocopy SKHGQLIKNFTVLQGPPSP<QCPKGDRGSQGLPGPTGNKGQKGEKGEPGPPGPVGERGPMGPVGPPGECG

Parental  SKGSKGSQGPKGSRGSPGKPGPQGPSGDPGPPGPPGKEGLPGPHGPPGFQGLQGTVGEPGVPGPRGLPGL
          SKGSKGSQGPK.S.GSPGKPGPQGPSGDPGPPGP..KEGLPGPH.PPGFQGLQGT.GEPGVPGP.GLPGL
Retrocopy SKGSKGSQGPKDSHGSPGKPGPQGPSGDPGPPGPLCKEGLPGPHSPPGFQGLQGTMGEPGVPGPWGLPGL

Parental  P-GVPGMPGPKGPPGPPGPSGAVVPLALQNEPTPAPEDNGCPPHWKNFTDKCYYFSVEKEIFEDAKLFCE
          P.G......P...P.PP.PSGAVVPLALQNEPTPAPEDNGCPPHWKNFTDKCYYFS.EKEIFEDAKLFCE
Retrocopy P>GYQACQDPR-VPRPPSPSGAVVPLALQNEPTPAPEDNGCPPHWKNFTDKCYYFSIEKEIFEDAKLFCE

Parental  DKSSHLVFINTREEQQWIKKQMVGRESHWIGLTDSENENEWKWLDGTSPDYKNWKAGQPDNWGHGHGPGE
          DKSSHLVFINTREEQQWIKKQMVGR.SHWIGLTDSENENEWKWLDGT.PDYK.WKAGQPDNWGHG.G.GE
Retrocopy DKSSHLVFINTREEQQWIKKQMVGRQSHWIGLTDSENENEWKWLDGTFPDYKSWKAGQPDNWGHGRGSGE

Parental  DCAGLIYAGQWNDFQCEDINNFICEKDRETVLSSAL
          DCAGLIYAGQWNDFQCEDINNFICEKDRETVLSS.L
Retrocopy DCAGLIYAGQWNDFQCEDINNFICEKDRETVLSSVL

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	1.07 RPM	26.56 RPM
SRP051959_kidney	0.29 RPM	10.56 RPM
SRP051959_liver	0.13 RPM	1.47 RPM
SRP051959_lung	0.10 RPM	50.27 RPM
SRP051959_lymph_node	0.00 RPM	6.58 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.75 RPM
SRP051959_spleen	0.02 RPM	5.38 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3363 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3363 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3363 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,