RetrogeneDB ID: retro_cjac_2771

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:135078985..135079465(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFT2D2
• Ensembl ID: ENSCJAG00000016838
• Aliases: None
• Description: SFT2 domain containing 2 [Source:HGNC Symbol;Acc:25140]

Sequence

>retro_cjac_2771
ATTGACAGGCTGAAGAAGGTGTTGAGCGGGCAGGACACGGAGGACCGGAGCGGCCTGTCCGAGGTTGTTGAGGCATCTTC
GTTAAGCTGGGGTACCAGGATAAAAGGCTTCATTGCGTGTTTTCCTATAGGAATTCTCTGCTCACTGCTGGGTACTTTTC
TGCTGTGGGTGCCCAGGAAGGGACTACACCTCTTCGCAGTGTTTTATACCTTTGGTAACATCGCATCAATTGGGAGTACC
ATCTTCCTCATGGGGCCACTGAAACAGCTGAAGCGGATGTTTGAGACTACATGTCTGATTGCAACTGTCATGGTGCTGTT
GTGTTTTGCACTTACCCTGTGTTCTGCCTTTTGGTGGCATAACAAGGGACTTGCACTTATCTTCTGCATTTTGCAGTCTT
TGGCATTGACATGATATAGCCTTTCCTTCATACCATTTGCAAGGGATGCTGTGAAGAAGTGTTTTGCCGTGTGTCTCGCA

Alignment

ORF - retro_cjac_2771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDKLKKVLSGQDTEDRSGLSEVVEASSLSWGTRIKGFIACFAIGILCSLLGTFLLWVPRKGLHLFAVFYT
          .D.LKKVLSGQDTEDRSGLSEVVEASSLSWGTRIKGFIACF.IGILCSLLGTFLLWVPRKGLHLFAVFYT
Retrocopy IDRLKKVLSGQDTEDRSGLSEVVEASSLSWGTRIKGFIACFPIGILCSLLGTFLLWVPRKGLHLFAVFYT

Parental  FGNIASIGSTIFLMGPLKQLKRMFEPTRLIATIMVLLCFALTLCSAFWWHNKGLALIFCILQSVALTWYS
          FGNIASIGSTIFLMGPLKQLKRMFE.T.LIAT.MVLLCFALTLCSAFWWHNKGLALIFCILQS.ALT.YS
Retrocopy FGNIASIGSTIFLMGPLKQLKRMFETTCLIATVMVLLCFALTLCSAFWWHNKGLALIFCILQSLALT*YS

Parental  LSFIPFARDAVKKCFAACLA
          LSFIPFARDAVKKCFA.CLA
Retrocopy LSFIPFARDAVKKCFAVCLA

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	0.09 RPM	12.20 RPM
SRP051959_heart	0.04 RPM	4.05 RPM
SRP051959_kidney	0.18 RPM	16.24 RPM
SRP051959_liver	0.06 RPM	5.50 RPM
SRP051959_lung	0.08 RPM	7.91 RPM
SRP051959_lymph_node	0.21 RPM	8.95 RPM
SRP051959_skeletal_muscle	0.02 RPM	3.43 RPM
SRP051959_spleen	0.13 RPM	5.88 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2771 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2771 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2771 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010720	1 retrocopy	retro_acar_131,
Callithrix jacchus	ENSCJAG00000016838	1 retrocopy	retro_cjac_2771 ,
Monodelphis domestica	ENSMODG00000002896	1 retrocopy	retro_mdom_607,
Mustela putorius furo	ENSMPUG00000000531	1 retrocopy	retro_mputfur_1560,
Nomascus leucogenys	ENSNLEG00000014912	1 retrocopy	retro_nleu_2370,
Rattus norvegicus	ENSRNOG00000003038	1 retrocopy	retro_rnor_1135,
Sarcophilus harrisii	ENSSHAG00000018938	1 retrocopy	retro_shar_212,
Ictidomys tridecemlineatus	ENSSTOG00000022560	1 retrocopy	retro_itri_133,