RetrogeneDB ID: retro_cjac_3473

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01181120.1:4858..6624(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_cjac_3473
AGTCAACTAAAAGAAACTTTGGAGAATAACTTCCCTCATCACCACTGTAAACAAAACCCTCCAGGCGTACAATGGCTATG
TCACGAATCTGCAGCAAGATACCAGTGTGCTCCAGGGTAATCTGCAGAACCAAATGTATTCTCATAACGTGGTCATCATG
AACCTCAACAACCTGAACCTGACCCAGGTACAGCAGAGGAACCTCATCATGAATCTGCAGCGGTCTGTGGATGACACAAG
CCAGGCTATCCAGCAAATCAAGAATGACTTTCAAAATCTGCAGCAGGTTTTTCTTCAAGCCAAGAAGGACACAGATTGAC
TGAAGGAGGAAGTGCAAAGCTTGCAGATGCTGGCTACCAATAATTCTGCTTTGGCCAAAGCCAACAACAACACCCTGGAG
GATATGAACAGCCAGCTCAACTCATTTACAGATCTGATGGAGAACATCACTATCTCTCAGGCCAACGAGCAGAACCTGAA
AGACCTGCAGAACTTACACAAGGATGCAGAGAATAGAACGGCCATCAGGTTCAACCAACTGGAGGAACACTTCCAGCTCT
TTGAGATGGATATTGTAAATATCATTAGCAATATCAGTTACACAGCCCACCACCTGGAGATGCTGACTAGCAATCTGAAT
GAAGTCAGGACCACTTGCATGGATACCCTAACCAAACACAAGGATGATCTGACTTCCTTGAATAATACCCTGGCCAACAT
CTGTTTGGATTCTGTTTCTCTCAGGATGCAACAAGTTTTGATGAGAGTGAGATTAGACACTGAAGTAAGCAACTTATCAG
TGATTATGGAAGAAATGAAGCTAGTAGACTCCAAGCATGGTCAGCTCATCAAGAATTTTACAATACTGCAAGGTCCACCC
AGCCCCAGTGTCCAAAAGGTGACAGAGGATCCCAGGGACCCCCTGGTCCAACTGGCAACAAGGGACAGAAAGGAGAGAAG
GGGGAACCTGGACCACCCGGCCCTGTGGGTGAGAGAGGCCCAATGGGACCAGTCGGTCCCCCTGGAGAGTGTGGCAGCAA
AGGCTCTAAAGGCTCCCAGGGACCCAAAGACTCCTGTGGTTTCCCCAGGAAGCCCGGCCCCAGGGCCCCAGTGGTGACCC
AGGCCCCCCAGGCCCACCGTGCAAAGAAGGACTCCCTGGCCCCCATGGCCCTCCTGGCTTCCAGGGACTACAGGGCACCA
TGGGGGAGCCTGGGGTGCCTGGACCTCGGGGACTGCCAGGTTTGCCTGGGGTACCAGGCATGCCAGGGCCCAAGGGTCTC
CCTGACCCCCCAGCCCATCAGAAGCAGTGGTGCCCCTGGCCCTGCAGAATGAGCCCACCCCTGCACCAGAGGATAATGGC
TGCCTGCCTCACTGGAAGAACTTCACAGACAAATGCTACTATTTTTCTGTTGAGAAAGAAATTTTTGAGGATGCAAAGCT
TTTCTGTGAAGACAAGTGTTCACATCTCATTTTCATAAACACTAGAGAAGAACAGCAATGGATTAAAAAACAGATGGTAG
GGAGAGAGAGCCACTGGATCTGCCTCAGACTCAGAGAATGAAAATGAATGGAAGTGGCTGGATGGGGCATCTCCAGACTA
CAAAAGTTGGAAAGCTGGACAGCCAGATAACTGGGGTCATGGCCATGGGCCAGGAGAAGACTGTGCTAGGTTGATTTATG
CTGGGCAGTGGAACGATTTCCAGTGTGAAGACATCAATAACTTCATTTGTGAAAAAGTCAGGGAGACAGTATTATCATCT
GCATTA

Alignment

ORF - retro_cjac_3473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.76 %
• Parental protein coverage: 79.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SQLKETLENNSF-LITTVNKTLQAYNGYVTNLQQDTSVLQGNLQNQMYSHNVVIMNLNNLNLTQVQQRNL
          SQLKETLE.N.F.LITTVNKTLQAYNGYVTNLQQDTSVLQGNLQNQMYSHNVVIMNLNNLNLTQVQQRNL
Retrocopy SQLKETLE-NNF>LITTVNKTLQAYNGYVTNLQQDTSVLQGNLQNQMYSHNVVIMNLNNLNLTQVQQRNL

Parental  ITNLQRSVDDTSQAIQRIKNDFQNLQQVFLQAKKDTDWLKEKVQSLQMLATNNSALAKANNDTLEDMNSQ
          I.NLQRSVDDTSQAIQ.IKNDFQNLQQVFLQAKKDTD.LKE.VQSLQMLATNNSALAKANN.TLEDMNSQ
Retrocopy IMNLQRSVDDTSQAIQQIKNDFQNLQQVFLQAKKDTD*LKEEVQSLQMLATNNSALAKANNNTLEDMNSQ

Parental  LNSFTGQMENITTISQANEQNLKDLQDLHKDAENRTAIKFNQLEERFQLFETDIVNIISNISYTAHHLRT
          LNSFT..MENIT.ISQANEQNLKDLQ.LHKDAENRTAI.FNQLEE.FQLFE.DIVNIISNISYTAHHL..
Retrocopy LNSFTDLMENIT-ISQANEQNLKDLQNLHKDAENRTAIRFNQLEEHFQLFEMDIVNIISNISYTAHHLEM

Parental  LTSNLNEVRTTCTDTLTKHTDDLTSLNNTLANIRLDSVSLRMQQDLMRSRLDTEVANLSVIMEEMKLVDS
          LTSNLNEVRTTC.DTLTKH.DDLTSLNNTLANI.LDSVSLRMQQ.LMR.RLDTEV.NLSVIMEEMKLVDS
Retrocopy LTSNLNEVRTTCMDTLTKHKDDLTSLNNTLANICLDSVSLRMQQVLMRVRLDTEVSNLSVIMEEMKLVDS

Parental  KHGQLIKNFTILQGPPGP-RGPKGDRGSQGPPGPTGNKGQKGEKGEPGPPGPAGERGPMGPVGPPGERGS
          KHGQLIKNFTILQGPP.P...PKGDRGSQGPPGPTGNKGQKGEKGEPGPPGP.GERGPMGPVGPPGE.GS
Retrocopy KHGQLIKNFTILQGPPSP<QCPKGDRGSQGPPGPTGNKGQKGEKGEPGPPGPVGERGPMGPVGPPGECGS

Parental  KGSKGSQGPKGSRGSPGKPGP-QGPSGDPGPPGPPGKEGLPGPHGPPGFQGLQGTVGEPGVPGPRGLPGL
          KGSKGSQGPK.S.G.P.KPGP.QGPSGDPGPPGPP.KEGLPGPHGPPGFQGLQGT.GEPGVPGPRGLPGL
Retrocopy KGSKGSQGPKDSCGFPRKPGP<QGPSGDPGPPGPPCKEGLPGPHGPPGFQGLQGTMGEPGVPGPRGLPGL

Parental  PGVPGMPGPKGPPGPPG-PSGAVVPLALQNEPTPAPEDNGCPPHWKNFTDKCYY-FSVEKEIFEDAKLFC
          PGVPGMPGPKG.P.PP..PS.AVVPLALQNEPTPAPEDNGC.PHWKNFTDKCYY.F...K..F.....F.
Retrocopy PGVPGMPGPKGLPDPPA<PSEAVVPLALQNEPTPAPEDNGCLPHWKNFTDKCYY>FLLRKK-FLRMQSFS

Parental  EDKSSHLVFINTREEQQWIKKQMVGRESHWIGLTDSENENEWKWLDGTSPDYKNWKAGQPDNWGHGHGPG
          ...S.H..F..T.E......K.....E.......DSENENEWKWLDG.SPDYK.WKAGQPDNWGHGHGPG
Retrocopy VKTSVHISFS*TLEKNSNGLKNRW*GERATGSASDSENENEWKWLDGASPDYKSWKAGQPDNWGHGHGPG

Parental  EDCAGLIYAGQWNDFQCEDINNFICEKDRETVLSSAL
          EDCA.LIYAGQWNDFQCEDINNFICEK.RETVLSSAL
Retrocopy EDCARLIYAGQWNDFQCEDINNFICEKVRETVLSSAL

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	0.04 RPM	26.56 RPM
SRP051959_kidney	0.33 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_3473 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3473 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3473 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,