RetrogeneDB ID: retro_rnor_1897

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:92495619..92496202(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dscr3
• Ensembl ID: ENSRNOG00000001681
• Aliases: None
• Description: Down syndrome critical region protein 3 [Source:RefSeq peptide;Acc:NP_001101786]

Sequence

>retro_rnor_1897
ACTCTGGACACCTACATTAAAAGGGTGAATAAAGTGTATCATGCTGTGGAAATGCTCTCTGGTATGGTGGTCATCTCTAG
CAAGGAGTCATTCCAGCACCAGGGAGTCTCTTTGACAATGGAAGGAATTATTAACCTCCAGCTCAGTGCCAAAAGTGGGG
TGTGTTTGAAACCTTTTGCAAACTCTGTGAAGCTGATCCAGTTTATCAACAGACCCACAGATGTGCTGAAGCCAGGAAAG
ATTCCCAGTGGCAAGACTGAGTTTCCCTCTGAGTTTCCTCTGCTTGTGAAATGCAGCAAGGTCCTGTATGAGACTTACCA
CCGCATGTTTGTGAACATTCAGTATACACTGCACTGTGACATGCGGCCGTCCCTATTGGTCAAGGACCTGACCAAGACCT
GTGAATTCACTGTTCACTCTGCTCCCCAGAAGTGGAAGGTATCCCCATGTCTTATTGACTTCATGATCACCTCAGAAATC
TTGCAGAACGTCAGGGAGGGCTTCACTTCCCAAATCCTTCATCAGAGCACATCTGAACTCTACTAACAGTGCTATCACGC
AGCCCCTTAGAGGAGAGCAGGTG

Alignment

ORF - retro_rnor_1897 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.41 %
• Parental protein coverage: 65.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLDIKIKRANKVYHAGEMLSGVVVISSKDSVQHQGVSLTMEGTVNLQLSAKSVGVFEAFYNSVKPIQIIN
          TLD..IKR.NKVYHA.EMLSG.VVISSK.S.QHQGVSLTMEG..NLQLSAKS......F.NSVK.IQ.IN
Retrocopy TLDTYIKRVNKVYHAVEMLSGMVVISSKESFQHQGVSLTMEGIINLQLSAKSGVCLKPFANSVKLIQFIN

Parental  STIDVLKPGKIPSGKTEVPFEFPLLVKGSKVLYETYHGVFVNIQYTLRCDMRRSLLAKDLTKTCEFIVHS
          ...DVLKPGKIPSGKTE.P.EFPLLVK.SKVLYETYH..FVNIQYTL.CDMR.SLL.KDLTKTCEF.VHS
Retrocopy RPTDVLKPGKIPSGKTEFPSEFPLLVKCSKVLYETYHRMFVNIQYTLHCDMRPSLLVKDLTKTCEFTVHS

Parental  A-PQKGKLTPSPVDFTITPETLQNVKERASLPKFLIRGHLNSTNCAITQPLTGELV
          A.P..G...P........P........RASLPK..IR.HLNSTN.AITQPL.GE.V
Retrocopy A>PRSGRY-PHVLLTS*SPQKSCRTSGRASLPKSFIRAHLNSTNSAITQPLRGEQV

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	16.10 RPM
SRP017611_kidney	0.00 RPM	28.75 RPM
SRP017611_liver	0.00 RPM	15.46 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1897 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1897 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1897 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002626	1 retrocopy	retro_cjac_2878,
Macropus eugenii	ENSMEUG00000007920	1 retrocopy	retro_meug_1828,
Nomascus leucogenys	ENSNLEG00000004717	1 retrocopy	retro_nleu_696,
Pan troglodytes	ENSPTRG00000013900	1 retrocopy	retro_ptro_2418,
Rattus norvegicus	ENSRNOG00000001681	1 retrocopy	retro_rnor_1897 ,