RetrogeneDB ID: retro_cjac_1142

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:40875645..40876579(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFNGR2
• Ensembl ID: ENSCJAG00000035211
• Aliases: None
• Description: None

Sequence

>retro_cjac_1142
TCCCGTCAGACTCTTTCCCAGCTGCCCGCTCCTCAGCACCAGAGGATTCACCGATACAATGAAGAACAGGTCCTGAGTTG
GGAGCCAGTGACCCTGAGCAATGGCACGAGGCCTGTGGTCTACTGGGTGCTGTTTAAATACAGCAGTGATGAATGGCTGA
CGGTGGACACGTCCATAGGGGTGAATTGTACCCAGATCACAGCGACAGAGTGTGACTTCACTGCCGCCAGCCCCTAAGCG
GGCTTCCCAATGGATTTCAATGTCACTCTACGCCTGCGAGCTGAACTGGGAGCACTCCATTCTGCCTGGGTGACAATGCC
TTGGTTTCAACACTATCGGAATGTGACAGTCGGGCCTCCAAAAAATATCGAGGTGACCCCAGGAGAAGGCTCCCTCATCA
TCAGATTCTCCTCTCCTTTTGAGATCCCTCATACCTCCACCGCCTGTTTTTGGTACTGTCAATTACTGGGAAGAAGCTGG
AGTCCAAAAGGTCAAAGGCCCTTTCAGAAGCAACTCCATTTCATTGGATAACTTAAAACCCTTCAGAGTGTACTGTTTAC
AAGCCCAGGCACAACTGCTTTGGAACAAAAGTAACGTAAATGGGCACTTAAGCAACACATCTTGCTACAAAATCATGGCA
GATGCCTCCGCCAAGCTTCCGCAAGTCATCCTGATCTCTGTGGGAACATTTGCGTAGATGTCAGTGCTGGCAGGGGCCTG
TTTCTTCCTGGTCCTGAAATACAGAGGCCTGATTAAATATTGGTTTCACACTCCACCAAGCATCCCATTACAGATAGAAG
AGTATTTAAAGGATCCTGCTCAGCCCATCTTAGATGACTTGGACAAGGACAGCTCACCAAGGGATGACGTCTGGGACTCT
GTGTCCATCATTTCATTTCCAGAAAAGGGGCAAGAAGATGTTCTCCAAACACAT

Alignment

ORF - retro_cjac_1142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.05 %
• Parental protein coverage: 94.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SQDSLSQLPTPQHPRIHLYNEEQVLSWEPVTLSNGTRPVVYRVQFKYSGDEWLTMDTSIGVNCTQITATE
          S...LSQLP.PQH.RIH.YNEEQVLSWEPVTLSNGTRPVVY.V.FKYS.DEWLT.DTSIGVNCTQITATE
Retrocopy SRQTLSQLPAPQHQRIHRYNEEQVLSWEPVTLSNGTRPVVYWVLFKYSSDEWLTVDTSIGVNCTQITATE

Parental  CDFTAASPSAGFPMDFNVTLRLRAELGALHSAWVTMPWFQHYRNVTVGPPKNIEVTPGEGSLVVRFSPPF
          CDFTAASP.AGFPMDFNVTLRLRAELGALHSAWVTMPWFQHYRNVTVGPPKNIEVTPGEGSL..RFS.PF
Retrocopy CDFTAASP*AGFPMDFNVTLRLRAELGALHSAWVTMPWFQHYRNVTVGPPKNIEVTPGEGSLIIRFSSPF

Parental  DIPDTSTACFWYY-IYYWEEAGVQKVKGPFRSNSISLDNLKPFRVYCLQVQAQLLWNKSNVNGHLSNTSC
          .IP.TSTACF..Y...YWEEAGVQKVKGPFRSNSISLDNLKPFRVYCLQ.QAQLLWNKSNVNGHLSNTSC
Retrocopy EIPHTSTACF-WY>VNYWEEAGVQKVKGPFRSNSISLDNLKPFRVYCLQAQAQLLWNKSNVNGHLSNTSC

Parental  YKIMADASTKLQQVILISVGTLSLMSVLAGACFFLVLKYRGLIKYWFHTPPSIPLQIEEYLKDPAQPILD
          YKIMADAS.KL.QVILISVGT...MSVLAGACFFLVLKYRGLIKYWFHTPPSIPLQIEEYLKDPAQPILD
Retrocopy YKIMADASAKLPQVILISVGTFA*MSVLAGACFFLVLKYRGLIKYWFHTPPSIPLQIEEYLKDPAQPILD

Parental  DLDKDSSPKDDVWDSVSIISFPEKGQEDVLQTH
          DLDKDSSP.DDVWDSVSIISFPEKGQEDVLQTH
Retrocopy DLDKDSSPRDDVWDSVSIISFPEKGQEDVLQTH

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	0.67 RPM	42.20 RPM
SRP051959_heart	0.16 RPM	9.56 RPM
SRP051959_kidney	0.35 RPM	19.39 RPM
SRP051959_liver	0.22 RPM	10.44 RPM
SRP051959_lung	0.31 RPM	14.01 RPM
SRP051959_lymph_node	0.25 RPM	10.16 RPM
SRP051959_skeletal_muscle	0.15 RPM	5.55 RPM
SRP051959_spleen	0.42 RPM	23.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1142 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1142 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1142 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	ENSCJAG00000035211	1 retrocopy	retro_cjac_1142 ,
Dasypus novemcinctus	ENSDNOG00000000695	1 retrocopy	retro_dnov_1882,
Tarsius syrichta	ENSTSYG00000008744	1 retrocopy	retro_tsyr_1201,