RetrogeneDB ID: retro_rnor_2782

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:33675185..33675877(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dnd1
• Ensembl ID: ENSRNOG00000016894
• Aliases: None
• Description: dead end protein homolog 1 [Source:RefSeq peptide;Acc:NP_001102849]

Sequence

>retro_rnor_2782
ATGCAGTCCAAACGGGAGTGTGTGCAATGGTGTGAGAGGGTGAATCCAGAGAACAAGGCAGCCCTAGAGGCGTGGATAAG
AGAGACTGGCATCCGCCTGGTGCAGGTCAACGGGCAAAGGAAGTATGGCGGGCCACCCTCAGGCTGGGTGGGCAGCCGGC
CACCGTCAGGGTCCGAGGTCTTTATCGGACGACTACCGCAGGATGTGTACGAGCACCAGCTGATCCCACTCTTCCAGCGC
GTGGGACGCCTCTATGAGTTCCGCCTAATGATGACCTTTAGTGGCCTGAACCGCGGCTTTGCCTATGCGCGCTACAGCTC
ACGGCGCGGTGCCCAGGCTTCCATTGCTACGCTGCACAACCACCAGTTGCGGCCTTCTTGCCAGCTCCTGGTATGCGAAG
TACCGAGAAGTGCGAGCTGACGGTGGACATGCTCCCTCTTAGCTTGAACCTACTGCTCGCCCTGCAACCGCTCGATCCCT
GCCTGCAGGAGACATTGCTGCTACAGAGCACTGGGTCTGAGCTCTCTCAAATTGCACTGCTCAAGTTTAGCACTCACTGA
GCTGCTGCCATGGCCAAAATGGCTCTGGTAGAAGGGCGGTCACGCCTCGGTGGAGAGTAGGTGGCTGTGAAGTGGCTCAA
GCCAGACCTGAAGCAGCACTTCCGCCAACAGCTTGCGGGTCCCTCACTGCGG

Alignment

ORF - retro_rnor_2782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.06 %
• Parental protein coverage: 66.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQSKRECEQWCERVNPENKAALEAWVRETGIRLVQVNGQRKYGGPPPGWVGSPPPSGSEVFIGRLPQDVY
          MQSKREC.QWCERVNPENKAALEAW.RETGIRLVQVNGQRKYGGPP.GWVGS.PPSGSEVFIGRLPQDVY
Retrocopy MQSKRECVQWCERVNPENKAALEAWIRETGIRLVQVNGQRKYGGPPSGWVGSRPPSGSEVFIGRLPQDVY

Parental  EHQLIPLFQRVGRLYEFRLMMTFSGLNRGFAYARYSSRRGAQAAIATLHNHQLRPSCQLLVC-RSTEKCE
          EHQLIPLFQRVGRLYEFRLMMTFSGLNRGFAYARYSSRRGAQA.IATLHNHQLRPSCQLLVC.RSTEKCE
Retrocopy EHQLIPLFQRVGRLYEFRLMMTFSGLNRGFAYARYSSRRGAQASIATLHNHQLRPSCQLLVC<RSTEKCE

Parental  LTVDGLPLSLNRRALLLALQPLGPCLQETLLLPSPGSAPSQIALLKFSTHRAAAMAKKALVEGQSRLCGE
          LTVD.LPLSLN...LLLALQPL.PCLQETLLL.S.GS..SQIALLKFSTH.AAAMAK.ALVEG.SRL.GE
Retrocopy LTVDMLPLSLN---LLLALQPLDPCLQETLLLQSTGSELSQIALLKFSTH*AAAMAKMALVEGRSRLGGE

Parental  QVAVEWLKPDLKQHFRQQLAGPSLR
          .VAV.WLKPDLKQHFRQQLAGPSLR
Retrocopy *VAVKWLKPDLKQHFRQQLAGPSLR

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	0.65 RPM
SRP017611_kidney	0.00 RPM	0.49 RPM
SRP017611_liver	0.00 RPM	0.27 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2782 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2782 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2782 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016345	1 retrocopy	retro_cjac_557,
Homo sapiens	ENSG00000256453	1 retrocopy	retro_hsap_1760,
Macropus eugenii	ENSMEUG00000016276	2 retrocopies	retro_meug_1326, retro_meug_614,
Mus musculus	ENSMUSG00000044595	1 retrocopy	retro_mmus_2548,
Pongo abelii	ENSPPYG00000015863	1 retrocopy	retro_pabe_1502,
Rattus norvegicus	ENSRNOG00000000204	1 retrocopy	retro_rnor_805,
Rattus norvegicus	ENSRNOG00000016894	1 retrocopy	retro_rnor_2782 ,