RetrogeneDB ID: retro_cjac_3944

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286373.1:219008..219386(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EFCAB2
• Ensembl ID: ENSCJAG00000016907
• Aliases: None
• Description: EF-hand calcium binding domain 2 [Source:HGNC Symbol;Acc:28166]

Sequence

>retro_cjac_3944
AGAGAGATTGGAACAATTATCAGGTCATTGGGATGCTGCCCTAGTGAAGGAGAGCTGCATGATCTGATTGCAGAGATAGA
GGAAGAAGAACCCACTGGATACATTCGATTTGAAAAATTTCTTCCGGTGATGACAGAAATACTACTAGAAAGAAGATACA
GACCCATTCCAGAAGATGTCCTTCTTCGAGCCTTTGAGGTTTTAGATACAGCTAACCGTGGGTTTCTTACTAAGAACGAA
TTGATCAAGTACATGACTGAAGAAGGTGAGCCTTTTTCTCAAGAGGAAATGGAAGAAATGTTGTCTGCTGCAATTGACCC
AGAATCAAATTCAATTAATTACAAGGACTATATATCAGTGATGGTGATAGATGAAAAT

Alignment

ORF - retro_cjac_3944 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.41 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  REIGTIIRSLGCCPSEGELHDLIAEIEEEEPTGYIRFEKFLPVMTEILLERRYRPIPEDVLLRAFEVLDT
          REIGTIIRSLGCCPSEGELHDLIAEIEEEEPTGYIRFEKFLPVMTEILLERRYRPIPEDVLLRAFEVLDT
Retrocopy REIGTIIRSLGCCPSEGELHDLIAEIEEEEPTGYIRFEKFLPVMTEILLERRYRPIPEDVLLRAFEVLDT

Parental  ANRGFLTKDELIKYMTEEGEPFSQEEMEEMLSAAIDPESNSINYKDYISMMVIDEN
          ANRGFLTK.ELIKYMTEEGEPFSQEEMEEMLSAAIDPESNSINYKDYIS.MVIDEN
Retrocopy ANRGFLTKNELIKYMTEEGEPFSQEEMEEMLSAAIDPESNSINYKDYISVMVIDEN

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	0.40 RPM	2.24 RPM
SRP051959_heart	0.46 RPM	4.53 RPM
SRP051959_kidney	0.67 RPM	5.70 RPM
SRP051959_liver	0.43 RPM	4.29 RPM
SRP051959_lung	0.57 RPM	4.93 RPM
SRP051959_lymph_node	0.73 RPM	3.54 RPM
SRP051959_skeletal_muscle	0.87 RPM	5.92 RPM
SRP051959_spleen	0.76 RPM	4.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3944 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3944 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3944 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029154	1 retrocopy	retro_cfam_781,
Callithrix jacchus	ENSCJAG00000016338	3 retrocopies	retro_cjac_106, retro_cjac_185, retro_cjac_316,
Callithrix jacchus	ENSCJAG00000016907	1 retrocopy	retro_cjac_3944 ,
Equus caballus	ENSECAG00000022403	1 retrocopy	retro_ecab_874,
Oryctolagus cuniculus	ENSOCUG00000029593	1 retrocopy	retro_ocun_612,
Tarsius syrichta	ENSTSYG00000006254	2 retrocopies	retro_tsyr_1584, retro_tsyr_317,