RetrogeneDB ID: retro_dnov_1557

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_23456:8566..9056(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF114
• Ensembl ID: ENSDNOG00000009113
• Aliases: None
• Description: ring finger protein 114 [Source:HGNC Symbol;Acc:13094]

Sequence

>retro_dnov_1557
CTCTGTCCCAGTACTCTGCGCACCCGGCATTCAAGCTGAGGAGCTTGAGCAGCAGATTTAAAGCACAGAGACTTCTTGCC
ATGGCTGCCAGAAAAAATTTCTTTCTCTCCAATATCCAGGCCCACATGACTACCTGTTCCAAATACCAGAATTACATCAT
GGAAGGTGTGAAGGCCACCATGAAGGATGCATCACTTTAGCCAAGGAATTTCCCAAACCATTATACCTTTCTTTGCCCTT
ATTGTCCTGAGAAGAACTTCGATCAGGAAGGACTTGTGGAACACTGCAAATTATCCCAAAGCACAGATAACAAATCTGTG
GTGTGTCCCATCTGTGCCTCAGTGCTCTGAGAAGACCCCAACTACCTCAGTGCCAACGTCATAGGGCATATCCAGTGCAG
CACTGTTTTCCTTAAAACACTTTTGTTGATTACAATGTGGATGAAGAAAGCACGATGAATCAGGTGTTTCAGCACTCCAT
CATTCATCAG

Alignment

ORF - retro_dnov_1557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.3 %
• Parental protein coverage: 70.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VCRSAL-APGVRAAELERQIESTETSCHGC-RKNFFLSKIRAHVATCSKYQNYIMEGVKATTKDASLQPR
          .C.S.L.APG..A.ELE.QI.STETSCHGC.RKNFFLS.I.AH..TCSKYQNYIMEGVKAT.KDASL.PR
Retrocopy LCPSTL>APGIQAEELEQQI*STETSCHGC>RKNFFLSNIQAHMTTCSKYQNYIMEGVKATMKDASL*PR

Parental  NVPNRYTFPCPYCPEKNFDQEGLVEHCKLSHSTDTKSVVCPICASMPWGDPNYRSANFIEHIQ-RRHQFS
          N.PN.YTF.CPYCPEKNFDQEGLVEHCKLS.STD.KSVVCPICAS....DPNY.SAN.I.HIQ...H.F.
Retrocopy NFPNHYTFLCPYCPEKNFDQEGLVEHCKLSQSTDNKSVVCPICASVL*EDPNYLSANVIGHIQ<VQHCFP

Parental  YDTFVDYDVDEEDMMNQVLQRSIIDQ
          ..TFVDY.VDEE..MNQV.Q.SII.Q
Retrocopy *NTFVDYNVDEESTMNQVFQHSIIHQ

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	16.72 RPM
SRP012922_cerebellum	0.00 RPM	12.92 RPM
SRP012922_heart	0.00 RPM	8.59 RPM
SRP012922_kidney	0.00 RPM	13.42 RPM
SRP012922_liver	0.00 RPM	12.23 RPM
SRP012922_lung	0.00 RPM	19.24 RPM
SRP012922_quadricep_muscle	0.00 RPM	9.35 RPM
SRP012922_spleen	0.00 RPM	31.36 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_1557 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 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009113	2 retrocopies	retro_dnov_1534, retro_dnov_1557 ,
Microcebus murinus	ENSMICG00000011155	1 retrocopy	retro_mmur_992,
Otolemur garnettii	ENSOGAG00000003953	3 retrocopies	retro_ogar_1149, retro_ogar_2158, retro_ogar_2330,
Ochotona princeps	ENSOPRG00000004732	2 retrocopies	retro_opri_368, retro_opri_709,
Pteropus vampyrus	ENSPVAG00000004117	4 retrocopies	retro_pvam_1136, retro_pvam_1148, retro_pvam_1149, retro_pvam_1477,
Sarcophilus harrisii	ENSSHAG00000001827	1 retrocopy	retro_shar_193,