RetrogeneDB ID: retro_dnov_1882

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_34879:1391..1977(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFNGR2
• Ensembl ID: ENSDNOG00000000695
• Aliases: None
• Description: interferon gamma receptor 2 (interferon gamma transducer 1) [Source:HGNC Symbol;Acc:5440]

Sequence

>retro_dnov_1882
CGGAATGTTACCATCGGGCCTCCAGAAAACATTTCGGTGACCCCAGGAGAAGGCTCACTGATCATCACGTTCTCCTCTCC
CTTTGACGTCACCACCTCCATGGTCACTCTTGAGTATCATATCCATTATTGGGGAAAAGAAGGAATTCAAGAGGTGAAAG
GCCCTTTCACAAGCAACTCCATTGTGTTGGTGAGTTTGAACTCTTAAGAGAATACTGTTGACAAGTCAAGGCAGAACTGA
TTTGGCCACAGCAAAACATCTGCAGACCCGGGCAGTTAAGCAACACATCTTGCTGTGAAACAGCAGCCAATGCCTCCACA
AAGCTTCAACCAGCCAAGCTGATCCTCATGGGAACCTCCCTGTTGGTGCTGGCACCAACCAAGTCTGTTGCTTCCTGATG
CTGAGATGCAGGGGCCTGATTAAATACTGGTTCCACTCTCCGCCCAGGATCCCATCGCAGAGAGAAGAGTATTTAAGGAA
CCCGGATCAGCCTACTTTAGAGGCCTTGAGCAAGGACAGCTCCCCAGAGGAGGATGCCTATGGCTCTCTGTCCATTGTTG
CCTTTCCAGAAGGGGAGAGAGAAGAT

Alignment

ORF - retro_dnov_1882 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.84 %
• Parental protein coverage: 64.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RNVTIGPPENISVTPGEGSLIIMFSSPFDVATSMVTLEYYIHYWEKEGIQEVKGPFIGNSIVL-GGLRPL
          RNVTIGPPENISVTPGEGSLII.FSSPFDV.TSMVTLEY.IHYW.KEGIQEVKGPF..NSIVL.G....L
Retrocopy RNVTIGPPENISVTPGEGSLIITFSSPFDVTTSMVTLEYHIHYWGKEGIQEVKGPFTSNSIVL<GEFELL

Parental  REYCLQVRAELIWPRQNICRPGQLSNTSCCETAANASAKLQQAIPIFAGTFLVVLALAGA-CYFLMLRYR
          REYC.QV.AELIWP.QNICRPGQLSNTSCCETAANAS.KLQ.A..I..GT.L.VLA.....C.FLMLR.R
Retrocopy REYC*QVKAELIWPQQNICRPGQLSNTSCCETAANASTKLQPAKLILMGTSLLVLAPTKS<CCFLMLRCR

Parental  GLIKYWFHSPPRIPSQIEEYLRNPDQPILEALSKDSSPEEDAYDSLSIVAFPEGERED
          GLIKYWFHSPPRIPSQ.EEYLRNPDQP.LEALSKDSSPEEDAY.SLSIVAFPEGERED
Retrocopy GLIKYWFHSPPRIPSQREEYLRNPDQPTLEALSKDSSPEEDAYGSLSIVAFPEGERED

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
SRP012922_ascending_colon	0.00 RPM	119.01 RPM
SRP012922_cerebellum	0.00 RPM	15.26 RPM
SRP012922_heart	0.00 RPM	33.41 RPM
SRP012922_kidney	0.00 RPM	15.88 RPM
SRP012922_liver	0.00 RPM	126.94 RPM
SRP012922_lung	0.00 RPM	80.64 RPM
SRP012922_quadricep_muscle	0.00 RPM	42.41 RPM
SRP012922_spleen	0.00 RPM	117.55 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_1882 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,