RetrogeneDB ID: retro_rnor_1772

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:57503264..57504202(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hormad1
• Ensembl ID: ENSRNOG00000021160
• Aliases: Hormad1, RGD1564960
• Description: HORMA domain-containing protein 1 [Source:UniProtKB/Swiss-Prot;Acc:D3ZWE7]

Sequence

>retro_rnor_1772
AAGTGGATGCTAGGATGCTATGATGCTTTACAGAAGAAATATCTAAGGATAATCATTCTAGCCGTATATACCAATCCAGA
AGATCCTCAGACAATTTCAGAATGTTACCAGTTTAAATTCAAGTACACCTAAAATGGACCAATCATGGACTCTATAAGCA
AAAAATCAAAACAATAACTCTAGTACAACATCTGCTTACACCAAGAAAGCAAGTATTCTCCTCATTCGGAAGATTTATGT
CCTAATGCAAAATCTAGGATCATTACCTAATGATGTTTGTCTGACAATGAAACTTTTTTACTACGATGAAGGTACACCCC
AAGATTACCAGCCACCAGGTTTTAAGGATGGTGATTGTGAAGGAGCAATATTTGATAGGGACCCTACATACTTAAATGTG
GGAGAAGTCCCAACACCTTCTCAACACCTTCAGATTAAAAGTGACCACTGAGAAGGAATGAATGGAAAATATTGATTCAG
CCATACTAACACCAAAAGATTAAAAAATGCCATTTCGAAAAATTCTAATGGACAAAGATGATGTAGAAAATGAAAATCAT
AGTAATTTTGACATTAAAACTAAAATGAACGAGCAGAATGAAAACTCTGGAACTTCTGAAATCAAAGAACCAAATTTAGA
TTGTAAGGAAGAAGAAATTATGCAATTCAAAAAGAACCAAAATCCTTCAATTTCTCAGTGTCAGCTTGAACAGTTAATCA
GTAAAACATCTGAACTTGATGTGTTTGAAAGCAAAACAAGAAGCGGAAAAATCTTTCAGTGCAAAATGGTAAATGGAAAT
CAACAAGGACGAGCTTCTAGAAAAAATCGGAAGAGAAGTCTTCGTCAATCTGGGAAAACAGTCCTTCATATCTTGGAATC
TTCTAGTCAAGAGTCGGTGCTGAAGAGAAGGAGAGTTAGTGAACCAAAGGAACATACC

Alignment

ORF - retro_rnor_1772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.76 %
• Parental protein coverage: 79.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KWMLGCYDALQKKYLRMIILAVYTNPEDPQTISECYQFKFKYTKNGPIMDFISK-NQNNKSSTTSADTKK
          KWMLGCYDALQKKYLR.IILAVYTNPEDPQTISECYQFKFKYT.NGPIMD.ISK.NQNN.SSTTSA.TKK
Retrocopy KWMLGCYDALQKKYLRIIILAVYTNPEDPQTISECYQFKFKYT*NGPIMDSISK>NQNNNSSTTSAYTKK

Parental  ASILLIRKIYVLMQNLGPLPNDVCLTMKLFYYDEVTPPDYQPPGFKDGDCEGVIFDGDPTYLNVGEVPTP
          ASILLIRKIYVLMQNLG.LPNDVCLTMKLFYYDE.TP.DYQPPGFKDGDCEG.IFD.DPTYLNVGEVPTP
Retrocopy ASILLIRKIYVLMQNLGSLPNDVCLTMKLFYYDEGTPQDYQPPGFKDGDCEGAIFDRDPTYLNVGEVPTP

Parental  -FHTFRLKVTTEKERMENIDSAILTPKDSKIPFQKILMDKDDVEDENHNNFDIKTKMNEQNENSGTSEIK
          ...TFRLKVTTEKE.MENIDSAILTPKD.K.PF.KILMDKDDVE.ENH.NFDIKTKMNEQNENSGTSEIK
Retrocopy >LNTFRLKVTTEKE*MENIDSAILTPKD*KMPFRKILMDKDDVENENHSNFDIKTKMNEQNENSGTSEIK

Parental  EPNLDCKEEEIMQFKKNQSSSISQCQVEQLISKTSELDVSESKTRSGKIFQCKMVNGNQQGQISKENRKR
          EPNLDCKEEEIMQFKKNQ..SISQCQ.EQLISKTSELDV.ESKTRSGKIFQCKMVNGNQQG..S..NRKR
Retrocopy EPNLDCKEEEIMQFKKNQNPSISQCQLEQLISKTSELDVFESKTRSGKIFQCKMVNGNQQGRASRKNRKR

Parental  SLRQSGKTVLHILESSSQESVLKRRRVSEPNEHT
          SLRQSGKTVLHILESSSQESVLKRRRVSEP.EHT
Retrocopy SLRQSGKTVLHILESSSQESVLKRRRVSEPKEHT

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
SRP017611_brain	0.00 RPM	0.22 RPM
SRP017611_kidney	0.00 RPM	0.21 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1772 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1772 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1772 has 0 orthologous retrocopies within eutheria group .

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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,