RetrogeneDB ID: retro_cjac_3860

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285268.1:37484..38009(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KITLG
• Ensembl ID: ENSCJAG00000019661
• Aliases: None
• Description: KIT ligand [Source:HGNC Symbol;Acc:6343]

Sequence

>retro_cjac_3860
TCTATCATAGACAAACTTGTGAACACATTGGATGACCTTATGGAGTGCGTGGAAGAAAACTCATCTAAGGATCTAAAAAA
ACCATTCAAGAGCCCAGAACCCAGGCTCTTTACTCCTGAAGAATTCTTTAGAATTTTTAATAGATCTTCAGATGCCTTTA
AGGACGTTGTAGTGGCATCTGAAACTAGTGATTGTATGGCTGCTTCAACATTAAGTCCTGAGAAAGAGTCCAGAGTCAGT
GCCACAAAACCATTGATGTTACCCTCTGTTGCAGCCAACTCCCTCAGGAATGACAGCAGTAGCGGTAATAGGAAGGCCAA
AAATCCCCCTGGAGATTCCGGCCTATACTGGGAAGCCATGGCATTGCCAGCCCTCTTTTCTCTTATAATTGGCTTTGCTT
TTGGAGCCTTATACTGGAAAAAGAGACAGCCAAGTCTTACAAGGACAGTTGAAAATACACGAACTAATGAAGAGGATAAT
GAGGTAATTATGCTGCAAGAGAAAGAAAGAGAATTTCAAGAAGTG

Alignment

ORF - retro_cjac_3860 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.71 %
• Parental protein coverage: 64.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SIIDKLVNIVDDLVECVKENSSKDLKKPFKSPEPRLFTPEEFFRIFNRSIDAFKDFVVASETSDCMASST
          SIIDKLVN..DDL.ECV.ENSSKDLKKPFKSPEPRLFTPEEFFRIFNRS.DAFKD.VVASETSDCMA.ST
Retrocopy SIIDKLVNTLDDLMECVEENSSKDLKKPFKSPEPRLFTPEEFFRIFNRSSDAFKDVVVASETSDCMAAST

Parental  LSPEKDSRVSVTKPFMLPSVAANSLRNDSSSSNRKAKNPPGDSGLHWAAMALPALFSLIIGFAFGALYWK
          LSPEK.SRVS.TKP.MLPSVAANSLRNDSSS.NRKAKNPPGDSGL.W.AMALPALFSLIIGFAFGALYWK
Retrocopy LSPEKESRVSATKPLMLPSVAANSLRNDSSSGNRKAKNPPGDSGLYWEAMALPALFSLIIGFAFGALYWK

Parental  KRQPSLTRTVENIQINEEDNEISMLQEKEREFQEV
          KRQPSLTRTVEN...NEEDNE..MLQEKEREFQEV
Retrocopy KRQPSLTRTVENTRTNEEDNEVIMLQEKEREFQEV

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	2.35 RPM
SRP051959_heart	0.00 RPM	4.82 RPM
SRP051959_kidney	0.00 RPM	7.06 RPM
SRP051959_liver	0.00 RPM	0.19 RPM
SRP051959_lung	0.00 RPM	23.70 RPM
SRP051959_lymph_node	0.00 RPM	0.64 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.70 RPM
SRP051959_spleen	0.08 RPM	0.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3860 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3860 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3860 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019661	2 retrocopies	retro_cjac_3502, retro_cjac_3860 ,
Oryctolagus cuniculus	ENSOCUG00000017687	1 retrocopy	retro_ocun_560,
Otolemur garnettii	ENSOGAG00000009638	1 retrocopy	retro_ogar_2863,