RetrogeneDB ID: retro_dnov_1938

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_3805:140746..141816(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBL1XR1
• Ensembl ID: ENSDNOG00000002317
• Aliases: None
• Description: transducin (beta)-like 1 X-linked receptor 1 [Source:HGNC Symbol;Acc:29529]

Sequence

>retro_dnov_1938
GATGGTACCTTGTTTGATGTTCGACCAATAGAATCCTTGTCACTAATAGATGCCAGTAATGCCTGATGTAGTACAAACAA
GACAAAAAGCTTATAGAGATAAACTTGCGCAGCAACAGGCAGCAGCTGCTGCAGCTACTGCAGCTGCAACAAACCAACAA
GGATCTGCAAAAAAATGGAGAAAACACAGCAAATGGGGAGGAAAATGGAGCACATACCATAGCAAATAATCACACTGATA
TGATGGAAGTGGACGGGGATGTTGAAATCCCGCCTAATAAAGCAGTGGTGTTACAGGGCCATGAATCTGAAGTTTTTATC
TGTGCCTGGAACCCTGTTAGTGATCTCCTGGCATCGGGGTCTGGAGATTCAACCGAAAGAATATGGAATCTTAGTGAAAA
TAGCACTAGTGGCTCCACACAGTTAGTACTTAGGCACTGTACACGAAAAGGAGGGCAAGATGTTCCAAGCAACAAGGATG
TAACATCTCTAGATTGGAATAGTGAAGGTACACTTCTAGCAAATGGTTCATATGATGGATTTGCCAGAATATGGACTAAA
GATGGTAATCTTGCTAGCACCTTGGGGCAGCATAAAGGCTCTATATTTGCATTAAAGTGGAATAAGAAAGGAAATTTCAT
CCTAAGTGCTGGAGTAGACAAGATTACAATTATTTGGGATGCACATACTGGTGAAGCCAAGCAAGTTTACTTTCATTCAG
CACAAGCACTGGTTGTTGATTGGCAAAGCAACAACACCTTTGTTTCTTGTAGTACAGATATGTACATTCATGTCTGTAAG
TTAGAACAAGACAGACCTATTAAAACATTTCAGGGACATACGAATGAAGAAAATGCTATCAAATGGGACCCAACTGGCAA
TCTTCTGACCTCCTGTTCTGAAGACATGACTTTAAAGATATGGAGTATGAAACAAGATAATTGTGTCCATAATTTGCAAG
CACATAATAAAGAAATTTATACCATCAAATGGAATCCAACAGGACCAGGAACAAATAATCCAAATGCCAACCTTATCTTA
GCAAGTGCATCCTTTGATTCTACTGTTAGG

Alignment

ORF - retro_dnov_1938 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.53 %
• Parental protein coverage: 70.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DGTLFDGRPIESLSLIDA-VMPDVVQTRQQAYRDKLAQQQAAAAAAAAAATNQQGSA-KNGENTANGEEN
          DGTLFD.RPIESLSLIDA.VMPDVVQTRQ.AYRDKLAQQQA.........TNQQGSA.KNGENTANGEEN
Retrocopy DGTLFDVRPIESLSLIDA>VMPDVVQTRQKAYRDKLAQQQAXXXXXXXXXTNQQGSA>KNGENTANGEEN

Parental  GAHTIANNHTDMMEVDGDVEIPPNKAVVLRGHESEVFICAWNPVSDLLASGSGDSTARIWNLSENSTSGS
          GAHTIANNHTDMMEVDGDVEIPPNKAVVL.GHESEVFICAWNPVSDLLASGSGDST.RIWNLSENSTSGS
Retrocopy GAHTIANNHTDMMEVDGDVEIPPNKAVVLQGHESEVFICAWNPVSDLLASGSGDSTERIWNLSENSTSGS

Parental  TQLVLRHCIREGGQDVPSNKDVTSLDWNSEGTLLATGSYDGFARIWTKDGNLASTLGQHKGPIFALKWNK
          TQLVLRHC.R.GGQDVPSNKDVTSLDWNSEGTLLA.GSYDGFARIWTKDGNLASTLGQHKG.IFALKWNK
Retrocopy TQLVLRHCTRKGGQDVPSNKDVTSLDWNSEGTLLANGSYDGFARIWTKDGNLASTLGQHKGSIFALKWNK

Parental  KGNFILSAGVDKTTIIWDAHTGEAKQQFPFHSAPALDVDWQSNNTFASCSTDMCIHVCKLGQDRPIKTFQ
          KGNFILSAGVDK.TIIWDAHTGEAKQ...FHSA.AL.VDWQSNNTF.SCSTDM.IHVCKL.QDRPIKTFQ
Retrocopy KGNFILSAGVDKITIIWDAHTGEAKQVY-FHSAQALVVDWQSNNTFVSCSTDMYIHVCKLEQDRPIKTFQ

Parental  GHTNEVNAIKWDPTGNLLASCSDDMTLKIWSMKQDNCVHDLQAHNKEIYTIKWSPTGPGTNNPNANLMLA
          GHTNE.NAIKWDPTGNLL.SCS.DMTLKIWSMKQDNCVH.LQAHNKEIYTIKW.PTGPGTNNPNANL.LA
Retrocopy GHTNEENAIKWDPTGNLLTSCSEDMTLKIWSMKQDNCVHNLQAHNKEIYTIKWNPTGPGTNNPNANLILA

Parental  SASFDSTVR
          SASFDSTVR
Retrocopy SASFDSTVR

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	2.53 RPM	17.11 RPM
SRP012922_cerebellum	0.96 RPM	5.36 RPM
SRP012922_heart	0.23 RPM	3.71 RPM
SRP012922_kidney	0.00 RPM	3.83 RPM
SRP012922_liver	0.62 RPM	4.02 RPM
SRP012922_lung	1.22 RPM	7.03 RPM
SRP012922_quadricep_muscle	0.69 RPM	6.40 RPM
SRP012922_spleen	1.60 RPM	15.11 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_1938 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	ENSDNOG00000002317	1 retrocopy	retro_dnov_1938 ,
Monodelphis domestica	ENSMODG00000021312	1 retrocopy	retro_mdom_8,