RetrogeneDB ID: retro_cjac_1231

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:82365454..82365950(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMP2
• Ensembl ID: ENSCJAG00000017147
• Aliases: None
• Description: epithelial membrane protein 2 [Source:HGNC Symbol;Acc:3334]

Sequence

>retro_cjac_1231
ATGTTGGTGCTTCCTGCTTTCGTCATGGCCCTCCACATCACCTCTGCGGCCTTGCTGTTCATCGCTACCATCGACAATGG
CTGGTGGGTAGATGAGTTTCTTGCAGATGTCTGGAGAATATGTAGCAACCACATGAATTGTACAGGAATCAGTGACAGCT
TTAAAGGGTCCTCCATGCTGCAGGTGACCCAGGCCACCATGATTCTCTCCATCCACCATTCTCTGCTGTACTGCCTTCTT
TGTCTTCGTGTTCCAGCTCTTCCACCTGAAGCAGGGAGAGAGGTTTGTCCTAACTTCCGTCATCCAGCTAATGTCATGTC
TGTATGTCATGATTGCAGCCTCCATTTATACAGACAGGCGTGAAGACATTCATGATAAAACACAGAATTCTATTACCTGA
CCAAAGGCAGCAGCTATGGCTACTCCTACATCCTGGTGAGGGTGGCCTTTGCCATCATCTTCATCCGTGGCAATGATGTA
CTCGATACTGAGGAAG

Alignment

ORF - retro_cjac_1231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.96 %
• Parental protein coverage: 98.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLVLLAFIIAFHITSAALLFIATIDNAWWVGDEFFADVWRICTNTTNCTVINDSFQEYSTLQAVQATMIL
          MLVL.AF..A.HITSAALLFIATIDN.WWV.DEF.ADVWRIC.N..NCT.I.DSF...S.LQ..QATMIL
Retrocopy MLVLPAFVMALHITSAALLFIATIDNGWWV-DEFLADVWRICSNHMNCTGISDSFKGSSMLQVTQATMIL

Parental  S-TILCC-IAFFIFLLQLFRLKQGERFVLTSIIQLMSCLCVMIAASIYTDRREDIHKK-NTEFYNLTEGG
          S.....C..AFF.F..QLF.LKQGERFVLTS.IQLMSCL.VMIAASIYTDRREDIH.K.NTEFY.LT.G.
Retrocopy S>STILCCTAFFVFVFQLFHLKQGERFVLTSVIQLMSCLYVMIAASIYTDRREDIHDK<NTEFYYLTKGS

Parental  SYGYSYILAWVAFACTFISG-LMYLILRK
          SYGYSYIL..VAFA..FI.G..MY.ILRK
Retrocopy SYGYSYILVRVAFAIIFIRG>MMYSILRK

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	6.03 RPM
SRP051959_heart	0.00 RPM	10.52 RPM
SRP051959_kidney	0.00 RPM	4.59 RPM
SRP051959_liver	0.00 RPM	18.30 RPM
SRP051959_lung	0.03 RPM	67.49 RPM
SRP051959_lymph_node	0.00 RPM	1.67 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.83 RPM
SRP051959_spleen	0.00 RPM	5.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1231 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1231 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1231 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017147	1 retrocopy	retro_cjac_1231 ,
Macropus eugenii	ENSMEUG00000000453	1 retrocopy	retro_meug_883,
Macaca mulatta	ENSMMUG00000008468	1 retrocopy	retro_mmul_1373,