RetrogeneDB ID: retro_dnov_2620

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_91298:6434..7311(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HORMAD1
• Ensembl ID: ENSDNOG00000000071
• Aliases: None
• Description: HORMA domain containing 1 [Source:HGNC Symbol;Acc:25245]

Sequence

>retro_dnov_2620
ATAGTTGTTCTAGCTGTATACACCAATCCAGAAGACCCTCAGACAATTTCAGAATGTTACCAGTTTAAATTCAAGTATAC
CAGTAGTGGACCAGTAATGGACTTTATAAGTAAAAACCAAAGTAATGAATCTAGCATGTCATCTGCTGACACTAAGAAAG
CAAGTATTCTCCTCATTCGCAAGATTTATATTCTAATGCAAAATCTGGGACCTTTACCTAATCATGTTTGTTTGACCATG
AAACTTTTTTACTATGATGAAGTTACACCCCCAGATTACCAACCTCCTGGTTTTAAGGATGGTGGTTGTGAAGGAGTGAT
ATTTGAAGGAGAACCTATGTACTTAAATGTGGGAGAAGTTCCAACAGTTTTTCACACCTTCAAAGTAAAAGTGACCACCG
AGAAAGAAAGAATGGAAAACTTTGATTCAGCTATACTATCACCAAAACAAATAAAAACACCACTTCAAAAAATCCTGATG
GACAAAGATGATCTAGAAGATGAACAAGAGCATTATATAAGTGATGATTTTGATACTGAATCTAAAATGGAAGAAAAAAA
AAAGCCCCTGGATCTTCTGAACTTGGAGAACTAAGTTTAGTTTGTGAGGAAGATGAAATTATGAGGTCTAAGGAAAGTCC
AGATCTTTCCATTTCTCATTCTCAGGTTGAGAAGTTAGTCAGTAAAACATCTGAACTTGATGTATCTGAAAGCAAAACAA
GAAGTGGAAAAATCTTTCCGAATCAAATGGTTAACGGAACTCAACCAGTAAAATCTTCTAAAGAAAATTAGAAGAGAAGT
CAACCTGAATCAGGGAAAAAGTTCTCCATCACTTTGATTCTTCTAGTCAGGAGTCAGTGTCAAAAAGGAGAAAGTTT

Alignment

ORF - retro_dnov_2620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.05 %
• Parental protein coverage: 75.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LMELIVYTNPEDPQTISECYQFKFKYTSSGPVMDFISKNQSNEPSMSSADTKKASILLIR-IYILMQNLG
          ...L.VYTNPEDPQTISECYQFKFKYTSSGPVMDFISKNQSNE.SMSSADTKKASILLIR.IYILMQNLG
Retrocopy IVVLAVYTNPEDPQTISECYQFKFKYTSSGPVMDFISKNQSNESSMSSADTKKASILLIRKIYILMQNLG

Parental  PLPND-CLTMKLFYYXXXXXXXXXXXXXXVGVFEGVIFEGRPYLNGGGEVPTPFHTFKVKVTTEKERMEN
          PLPN..CLTMKLFYY...............G..EGVIFEG.P.....GEVPT.FHTFKVKVTTEKERMEN
Retrocopy PLPNHVCLTMKLFYYDEVTPPDYQPPGFKDGGCEGVIFEGEPMYLNVGEVPTVFHTFKVKVTTEKERMEN

Parental  IDSAILSPKQIKTPLQKILVDKDDLEDEQEHYISDDFDTESKME-EQKKAPGSSELGEPSLVCEEDEIMR
          .DSAILSPKQIKTPLQKIL.DKDDLEDEQEHYISDDFDTESKME.....APGSSELGE.SLVCEEDEIMR
Retrocopy FDSAILSPKQIKTPLQKILMDKDDLEDEQEHYISDDFDTESKME<XXXXAPGSSELGELSLVCEEDEIMR

Parental  SKESPDLSISHSQVEQLVSKTSELDVSESKTRSGKIFQNKMFNGIQPVKSSKENRKRSQPESGK-KVLHH
          SKESPDLSISHSQVE.LVSKTSELDVSESKTRSGKIF.N.M.NG.QPVKSSKEN.KRSQPESGK.KVLHH
Retrocopy SKESPDLSISHSQVEKLVSKTSELDVSESKTRSGKIFPNQMVNGTQPVKSSKEN*KRSQPESGK<KVLHH

Parental  FDSSSQESVSKXXXF
          FDSSSQESVSK...F
Retrocopy FDSSSQESVSKRRKF

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	0.00 RPM
SRP012922_cerebellum	0.14 RPM	0.14 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	0.55 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.46 RPM	0.61 RPM
SRP012922_quadricep_muscle	0.35 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	0.69 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_2620 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000071	1 retrocopy	retro_dnov_2620 ,
Homo sapiens	ENSG00000143452	1 retrocopy	retro_hsap_3612,
Mus musculus	ENSMUSG00000028109	2 retrocopies	retro_mmus_1420, retro_mmus_2717,
Otolemur garnettii	ENSOGAG00000005640	1 retrocopy	retro_ogar_1908,
Rattus norvegicus	ENSRNOG00000021160	1 retrocopy	retro_rnor_1772,
Tarsius syrichta	ENSTSYG00000006025	1 retrocopy	retro_tsyr_1426,