RetrogeneDB ID: retro_dnov_1887

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_35202:390..1170(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35F5
• Ensembl ID: ENSDNOG00000013643
• Aliases: None
• Description: solute carrier family 35, member F5 [Source:HGNC Symbol;Acc:23617]

Sequence

>retro_dnov_1887
CCAAGTGAAAAACCTGAGAGCACAAACATTGATACTGAAAAATCTCCCCAAAAGTCTCATGTAAGGTTGAGTAATATGGA
GATTTGGCAGTCTTCCTCAAGCCTTGCATTGGAAGCTAAGTTGTCATACATGTCATATCCTGCTGTGAAAGAACAGGAAT
CCATACAGAAATTGTGGGGGATTTTACTGCAACTCAAGTAGCAAAAATAAGCTCTTTTTTTTTCCTTTGTGCGATTTTGG
CAAATTTGTCATATCAAGCACTTTGAGACGCACAAGTTGCTGTAAGTTAATATTTTGTCTTCAACTTCTGGACTTTTTAC
CTTTTTCCTTGCTGGAGTGTTTCCAAGTTAACACTGAAAACACCAAGTTTACTCTTTCACACTATTAGTTGTAATTTTAT
CATTGGTTGTAGGGGATGTGCTGGTAAACCTGTCTAGGTCTGAAAAAACTGCTGGAAGAGATAGAACAGGTTCCTCATCT
CTTGTGGAGCCATGGTCTGTGCTGTCTATATTGTCATGATTAAGAGAAAAGTAGACAGAGAAGATAAGTTGATATCCCAA
TGTTTGGGTTTGTAGGTCTGTTTACTTTGGTGCTCTCATGGCCAGGTTTGTTTTTACTAATTATATTGGATTTGAATACT
TTGAGTTTCCCAGTAAAGTAGTATTAATGTCCATTATTGTTAATGGCCTTAATGGGACAGTTCTCTCCGAGTTCCTGTGC
TTGTAGGGCTGCTTTACATCATCAGTAAGCACACTTGCACTAAGCCTTACAATACCTCTC

Alignment

ORF - retro_dnov_1887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.07 %
• Parental protein coverage: 53.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  PSEKPESTNTDTEKTLKKSRVRFSNIMEIRQLPSSHALEAKLSRMSYPAVKEQESILKT-VGKLTATQVA
          PSEKPESTN.DTEK...KS.VR.SN.MEI.Q..SS.ALEAKLS.MSYPAVKEQESI.K..VG..TATQVA
Retrocopy PSEKPESTNIDTEKSPQKSHVRLSN-MEIWQSSSSLALEAKLSYMSYPAVKEQESIQKL<VGDFTATQVA

Parental  KISFFFCFVWFLANFSYQEALSDTQVAI-VNILSSTSGLFTLILAAV-FPSNSGD-RFTLSK-LLAVILS
          KIS........LAN.SYQ.AL.D.QVA..VNILSSTSGLFT..LA.V.F..N.....FTLS..LL.VILS
Retrocopy KISXXXXLCAILANLSYQ-AL*DAQVAV>VNILSSTSGLFTFFLAGV>FQVNTENTKFTLSH<LLVVILS

Parental  -IGGVVLVNLSGSEKSAGRNTIGSIWSLV-GAMLYAVYIVMIKRKVDREDKL-DIPMFFGFVGLFNLLLL
          ...G.VLVNLS.SEK.AGR...GS..SLV.GAM..AVYIVMIKRKVDREDKL.DIPMF.GFVGLF.L.L.
Retrocopy LVVGDVLVNLSRSEKTAGRDRTGSS-SLV<GAMVCAVYIVMIKRKVDREDKL<DIPMF-GFVGLFTLVLS

Parental  WPGFFLL-HYTGFEDFEFPNKVVLMCIVINGLIGTVLSEFLWLWGCFLTSSLIGTLALSLTIPL
          WPG.FLL..Y.GFE.FEFP.KVVLM.I..NGL.GTVLSEFL.L.GCF..S....TLALSLTIPL
Retrocopy WPGLFLL<NYIGFEYFEFPSKVVLMSIIVNGLNGTVLSEFLCL*GCFTSS--VSTLALSLTIPL

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	23.73 RPM
SRP012922_cerebellum	0.00 RPM	6.19 RPM
SRP012922_heart	0.00 RPM	9.75 RPM
SRP012922_kidney	0.00 RPM	20.81 RPM
SRP012922_liver	0.00 RPM	18.58 RPM
SRP012922_lung	0.00 RPM	14.20 RPM
SRP012922_quadricep_muscle	0.17 RPM	26.48 RPM
SRP012922_spleen	0.11 RPM	10.99 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_1887 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013643	1 retrocopy	retro_dnov_1887 ,
Erinaceus europaeus	ENSEEUG00000003303	1 retrocopy	retro_eeur_388,