RetrogeneDB ID: retro_cjac_26

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:68198271..68199204(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023059
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_cjac_26
AATAACTACTCCCACTTCCAACACCTTTACTTTGTCTTGACTGGAATTCCAGGGCTTGAGCAAAAGTACTATTGGATGGC
ATTCCCATTTGGTGCTATATATGTTGTTGCCCTCTTTGGCAATAGCATCATAATCTCTACCATCAAATCTGAGTCGTCTC
TACATATCCCTATGTACTACTTTCTGTGCATGCTGGCATTGGCAGACACGGGGCTTGCCCTCTGTACTTTGCCTTCTATG
CTAGGAATATTCTGGTTTAACTACAAGTCCATTGCCTTTGATGCCTGTCTTGTTCAGATGTACTTCATCCACACCTTCTC
AGCCATTGAGTCTGGGGTGCTGGTGGCAATGGCCTTTGATCGGGTTGTGGCAATCTGGAGCCCTCTCAGGTACAGTGTCA
TTCTAACCAATGGTGTGGTCTGCAAAACAGGGTTAGTCATCTTTTCAAGGGCAGTCTGTGTTGTCTTCCCTGTGCCTTTC
CTCATCAAGAGGCTCCCCTTCTACCACTCCAACATCCTCTCCCACTCCTTCTGCCTCCATCAAGATGTTATGCACCTTGC
CTGTGCCAGCACCCATGTCAACAGTCTCTATGGCCTCATCGCTGTCATCTTCACCAAGGGTTCTGACTCGCTATCCATCC
TTCTCTCCTATGTGTTTATACTTCGAACAGTAATGGCTATTGCCTCAAGGGAGGGTCGTCTGAAGGCACTCAACACCTGT
GTTTCACACATCTGTGCTGTACTCATCTTCTATGTGCCACTCATTGGGGTGTCTGTCATTCACCGCTTTGGAAAGCACCT
GTCACCACTGACTCATGTCCTCATGGCAAATGCCTACCTTCTTGTACCCCCTGTGCTAAACCCCATAGTCTATACTGTGA
AGACCAAAGAAATACGAAGGAAGATCATCCAGATATTTGTTCAAACCAAGATT

Alignment

ORF - retro_cjac_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.64 %
• Parental protein coverage: 98.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NSSEIEITTCFLIGIPGLEHAQVWISVPICLMYLVAIIGNCTILFVIRTEPSLHAPMYYFLSMLAVSDLG
          N.S........L.GIPGLE....W...P....Y.VA..GN..I...I..E.SLH.PMYYFL.MLA..D.G
Retrocopy NYSHFQHLYFVLTGIPGLEQKYYWMAFPFGAIYVVALFGNSIIISTIKSESSLHIPMYYFLCMLALADTG

Parental  LSLSSLPTMLRIFVFNATGVSPNACFAQEFFIHGFTVMESSVLLVMSLDRFLAIRNSLRYSSILTNSVFI
          L.L..LP.ML.IF.FN.......AC..Q..FIH.F...ES.VL..M..DR..AI...LRYS.ILTN.V..
Retrocopy LALCTLPSMLGIFWFNYKSIAFDACLVQMYFIHTFSAIESGVLVAMAFDRVVAIWSPLRYSVILTNGVVC

Parental  AIGIAIFTRAVCVVFPVPFLIKRLPFCHSNVLSHSYCLHQDMMRLACGSTHINSFYGLIVVIFTLGLDAL
          ..G..IF.RAVCVVFPVPFLIKRLPF.HSN.LSHS.CLHQD.M.LAC.STH.NS.YGLI.VIFT.G.D.L
Retrocopy KTGLVIFSRAVCVVFPVPFLIKRLPFYHSNILSHSFCLHQDVMHLACASTHVNSLYGLIAVIFTKGSDSL

Parental  LILMSYVLILKTVLGIASSGERLKTLSTCLSHMFAVLLFYVPFIGSSMIHRFGKHLPPVVHMLMANIYLL
          .IL.SYV.IL.TV..IAS...RLK.L.TC.SH..AVL.FYVP.IG.S.IHRFGKHL.P..H.LMAN.YLL
Retrocopy SILLSYVFILRTVMAIASREGRLKALNTCVSHICAVLIFYVPLIGVSVIHRFGKHLSPLTHVLMANAYLL

Parental  LPPVLNPIVYSVKTKQIRRRIIQVF
          .PPVLNPIVY.VKTK.IRR.IIQ.F
Retrocopy VPPVLNPIVYTVKTKEIRRKIIQIF

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	0.00 RPM	0.00 RPM
SRP051959_lymph_node	0.02 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_26 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_26 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_26 has 0 orthologous retrocopies within eutheria group .

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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 ,