RetrogeneDB ID: retro_cjac_1450

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:15801085..15801534(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISCA2
• Ensembl ID: ENSCJAG00000020479
• Aliases: None
• Description: iron-sulfur cluster assembly 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:19857]

Sequence

>retro_cjac_1450
ATGGCTGCCACTCTGGGGTTGTCCCCTAACAGCCCCGACACAGAACAGTCACTCCCTGGCTGAGGTGCAGGCTCCTTGTT
GCCTCCCTGGGACACTGGGCGCGTGGGAAAGGGACATCCTCCAGCCCCAAGGCCGGCGAAGGGCAGATCCGTCTCAGGGA
CGGCTGAGTCCAGAGGCTTCTGGAAATCACTGAAGGGTCAGAATTCTTCAGGCTGCAGGTGGAGGGAGGTGGATGCTCCA
GATTCCAATACAGACTTTCACTGGATACAGTTATCCACCCCAACAACGGGGTATTCGAACGGGGGCGGGGGGCAAGGGTG
GTGGTTGACTCTGATAGCTCGGCCTTCGTGAAAGGGGCCCAGGTGGACTTGGTCCAAGAACTGATCCGAAGCTCATTTGA
AGTACAGAGTAATCCTCAAGCACAGCAAGGCTGCTCCTGTGGGTCATCC

Alignment

ORF - retro_cjac_1450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.19 %
• Parental protein coverage: 96.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAVRGLSLTAAT-QKVVTHWPKGRLLAASLGLRARREASSSSPEAGEGQIRLTDSCVQRLLEITEGSEF
          MAA..GLS.........VT.W...RLL.ASLG..AR....SSSP.AGEGQIRL.D..VQRLLEITEGSEF
Retrocopy MAATLGLSPNSPD<HRTVTPWLRCRLLVASLGHWARGKGTSSSPKAGEGQIRLRDG*VQRLLEITEGSEF

Parental  LRLQVEGGGCSGFQYKFSLDTVINPDDRVFEQG-GARVVVDSDSLAFVKGAQVDFSQELIRSSFQVLNNP
          .RLQVEGGGCS.FQY..SLDTVI.P...VFE.G.GARVVVDSDS.AFVKGAQVD..QELIRSSF.V..NP
Retrocopy FRLQVEGGGCSRFQYRLSLDTVIHPNNGVFERGRGARVVVDSDSSAFVKGAQVDLVQELIRSSFEVQSNP

Parental  QAQQGCSCGSS
          QAQQGCSCGSS
Retrocopy QAQQGCSCGSS

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	5.44 RPM
SRP051959_heart	0.00 RPM	9.37 RPM
SRP051959_kidney	0.00 RPM	9.94 RPM
SRP051959_liver	0.00 RPM	7.95 RPM
SRP051959_lung	0.00 RPM	8.88 RPM
SRP051959_lymph_node	0.00 RPM	7.31 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.68 RPM
SRP051959_spleen	0.00 RPM	7.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1450 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1450 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1450 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020479	1 retrocopy	retro_cjac_1450 ,
Dipodomys ordii	ENSDORG00000014857	1 retrocopy	retro_dord_762,
Gorilla gorilla	ENSGGOG00000012894	1 retrocopy	retro_ggor_1610,
Macaca mulatta	ENSMMUG00000006566	1 retrocopy	retro_mmul_643,
Nomascus leucogenys	ENSNLEG00000016268	1 retrocopy	retro_nleu_2754,
Ochotona princeps	ENSOPRG00000011684	2 retrocopies	retro_opri_1068, retro_opri_124,
Pan troglodytes	ENSPTRG00000006536	1 retrocopy	retro_ptro_1504,
Rattus norvegicus	ENSRNOG00000012085	1 retrocopy	retro_rnor_1009,