RetrogeneDB ID: retro_dnov_1346

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_18483:46369..47104(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: S100PBP
• Ensembl ID: ENSDNOG00000000537
• Aliases: None
• Description: S100P binding protein [Source:HGNC Symbol;Acc:25768]

Sequence

>retro_dnov_1346
CCAGTAGCTGAGACCCCTGGCCTCTTTAGACTACATTAACTAAATACATCAGATGGTAATGGGCCAATCCCTACTAAACT
TTGCACAGACATTTTAAACCTGAAAAGAATCTTATGAAAATAACTGTTGTTGCAACATTTAATCCAACAGTTTATAATGC
TGTGCTTGATAAGCATAAAACAGATTTATCCAAAGATCAGAAAATCTTTTTTCCCTTGGGGAAGATATGAGAGAAGATGG
TCTTAGCACAAATGAGAGCAAAATTTGCTCTGAATCTGAATGAATCAACCCTACAAAGTTTGCCTGCAGTGAGCCCCTAT
CCCCTTCTCCTTTGAACAATGACTTTCAACGAAATGTCTGTGATAAAAAATAAGCCTAACAATAAAAAACTTTCACCTAT
ATTCTCTCAGGGCTTGGACAATTGAGAGAGTCCATCTACTAGGGGGTCACCATTGAGAAATGGTGGGTCACATAAATCAA
GTTATGAAATGAGGTGTTTGATTGTTTTCCAGTTCATCAGAAAAATGGGATGATTTTAACAGGGATTCTGTGAAGATGAA
TGTCAATGACAGACAACTAGGCAGAGTCATTCCTATTCTGCAAACCAAAACAAGGACTAATGTTATGACATTTTCACAGT
CAGATCTACCACAGCAGAAGCAAATTTATCTCAGGCATGTCATTGCTTATATAAAAGAACCAGTGGACTCTCATCAAGGT
TCCTTGAGGGAAATG

Alignment

ORF - retro_dnov_1346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.86 %
• Parental protein coverage: 58.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PVAETPDIFKLPQLSSSVGHGPAPTK-PLNRHFALEKNLIKITVVAPFNPTVSDAVLDKDKTDSSKDIK-
          PVAETP..F.L..L..S.G.GP.PTK..L.RHF..EKNL.KITVVA.FNPTV..AVLDK.KTD.SKD.K.
Retrocopy PVAETPGLFRLH*LNTSDGNGPIPTK<TLHRHFKPEKNLMKITVVATFNPTVYNAVLDKHKTDLSKDQK<

Parental  KSSSLGEDRREDGYSPNESKLCTESEGINPTNFAWDGPTVPSPLNNDFQQTNYDK-NTHDSKESSPVFSK
          ...SLGED.REDG.S.NESK.C.ESE.INPT.FA...P..PSPLNNDFQ....DK.N....K..SP.FS.
Retrocopy NLFSLGEDMREDGLSTNESKICSESE*INPTKFACSEPLSPSPLNNDFQRNVCDK>NKPNNKKLSPIFSQ

Parental  VLDHLESPSNMESSSRNGGSHKSNCETRFPVV-SSSSDKQDVLDKDSGKIKVNERRLGKVIPVPQTKTRT
          .LD..ESPS...S..RNGGSHKS..E.R...V.SSSS.K.D....DS.K..VN.R.LG.VIP..QTKTRT
Retrocopy GLDN*ESPSTRGSPLRNGGSHKSSYEMRCLIV>SSSSEKWDDFNRDSVKMNVNDRQLGRVIPILQTKTRT

Parental  NVSTFSRSDLEQQKEIYLRSVIAHIKDPVDSNQGPLREL
          NV.TFS.SDL.QQK.IYLR.VIA.IK.PVDS.QG.LRE.
Retrocopy NVMTFSQSDLPQQKQIYLRHVIAYIKEPVDSHQGSLREM

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	13.03 RPM
SRP012922_cerebellum	0.14 RPM	14.43 RPM
SRP012922_heart	0.00 RPM	2.55 RPM
SRP012922_kidney	0.00 RPM	6.30 RPM
SRP012922_liver	0.00 RPM	1.70 RPM
SRP012922_lung	0.00 RPM	11.45 RPM
SRP012922_quadricep_muscle	0.00 RPM	2.42 RPM
SRP012922_spleen	0.00 RPM	11.68 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_1346 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000537	1 retrocopy	retro_dnov_1346 ,
Erinaceus europaeus	ENSEEUG00000006053	1 retrocopy	retro_eeur_439,
Myotis lucifugus	ENSMLUG00000000764	1 retrocopy	retro_mluc_1691,
Monodelphis domestica	ENSMODG00000017396	2 retrocopies	retro_mdom_1633, retro_mdom_62,
Tursiops truncatus	ENSTTRG00000014993	1 retrocopy	retro_ttru_89,