RetrogeneDB ID: retro_cjac_25

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:68225272..68226136(+)
• Located in intron of: ENSCJAG00000015659

Retrocopy information

• Ensembl ID: ENSCJAG00000034160
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000015659
• Aliases: None
• Description: None

Sequence

>retro_cjac_25
TTCTTCATCCTGACTGGGATTCCAGAAATGCCAGAGAAGGACTTATGGATGGCCTTGCCTCTCTGTCTTCTTTACAGTAC
TACAATCCCGGGAAATGTCACCATCCTAGTTGTTATCAAAGTTGAGCAAAGTTTCCATGAACCCATGTATTATTTTCTAG
CCATGTTAGCTGCCACTGACCTCAGCCTTTCACTGTCTTCCATGCCTACCATGGTCAGTGTTCACTGGTTCAACCGGTGT
TCGAAAACTTTTAATGTCTGCCTTATCCAGATGTTCTTCATCCACACATTTGGGGGAGTGGAATCAGGTATTCTGGTGGC
CATGGCCTTTGATTGCTTTGTGGCCATCAGCTTTCCTTTGCGCTATGCTACCATTCTCACTCACAGTGTAATCAGCAAGA
TTGCAGCAGCAGTCCTGCTATGGAGTGTGGTAACTGTGCTCCCTGTGCCTTTTCTCATCAAAAGGTTACCTTTCTGCCAC
TCCAATGTCCTCTCCCATGCATACTGCCTCCATCAGGATGCCATGAGGCATGCCTGTGCTGACACCAATGTCAATATCAT
CTATGGCCTGCTGGCTGTGATCTTCATCATTGTACTAGATGCCTTGATACTTTTGGTCTCTTACATTCTAATCCTCCAGG
CAGTATTGGGCGTTGCTTCCCAGGAAGAGAGGCTCAAGGGTCTCAACACCTGCCTCTCTCATATCTGTGCAGTTATGCTT
TTCTATGTGCCTCTCATTGGCATGACCCTAATTCATTGCTATGGGAAGCATTTGCCACCAATAATACACACATTCATGGC
CGATATCTACCTGCTTCTCCCGCCTGTGCTCAATCCCATTGTGTACATTGTTAGGACCAAGTAG

Alignment

ORF - retro_cjac_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.15 %
• Parental protein coverage: 91.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIGIPGLEHAQVWISVPICLMYLVAIIGNCTILFVIRTEPSLHAPMYYFLSMLAVSDLGLSLSSLPTMLR
          L.GIP.......W...P.CL.Y...I.GN.TIL.VI..E.S.H.PMYYFL.MLA..DL.LSLSS.PTM..
Retrocopy LTGIPEMPEKDLWMALPLCLLYSTTIPGNVTILVVIKVEQSFHEPMYYFLAMLAATDLSLSLSSMPTMVS

Parental  IFVFNATGVSPNACFAQEFFIHGFTVMESSVLLVMSLDRFLAIRNSLRYSSILTNSVFIAIGIAIFTRAV
          ...FN......N.C..Q.FFIH.F...ES..L..M..D.F.AI...LRY..ILT.SV...I..A.....V
Retrocopy VHWFNRCSKTFNVCLIQMFFIHTFGGVESGILVAMAFDCFVAISFPLRYATILTHSVISKIAAAVLLWSV

Parental  CVVFPVPFLIKRLPFCHSNVLSHSYCLHQDMMRLACGSTHINSFYGLIVVIFTLGLDALLILMSYVLILK
          ..V.PVPFLIKRLPFCHSNVLSH.YCLHQD.MR.AC..T..N..YGL..VIF...LDAL..L.SY.LIL.
Retrocopy VTVLPVPFLIKRLPFCHSNVLSHAYCLHQDAMRHACADTNVNIIYGLLAVIFIIVLDALILLVSYILILQ

Parental  TVLGIASSGERLKTLSTCLSHMFAVLLFYVPFIGSSMIHRFGKHLPPVVHMLMANIYLLLPPVLNPIVYS
          .VLG.AS..ERLK.L.TCLSH..AV.LFYVP.IG...IH..GKHLPP..H..MA.IYLLLPPVLNPIVY.
Retrocopy AVLGVASQEERLKGLNTCLSHICAVMLFYVPLIGMTLIHCYGKHLPPIIHTFMADIYLLLPPVLNPIVYI

Parental  VKTK
          V.TK
Retrocopy VRTK

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	0.00 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.02 RPM	0.00 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_25 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_25 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_25 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015659	2 retrocopies	retro_cjac_25 , retro_cjac_26,