RetrogeneDB ID: retro_rnor_1080

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:108145164..108145659(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGD1564093
• Ensembl ID: ENSRNOG00000003863
• Aliases: None
• Description: None

Sequence

>retro_rnor_1080
GAGCCTCCGGGTCGGGAGGCGCCCGGCCCGGCGGGCAGCGGCAGGAGCCGATGGGCTGAGTCGGGGCCGGGAACATCACC
CGAGAGTGGGGATGACGAGGTGTAGGGCTCAAGTCCGGTGTCCAGCGGTGTGAACTTGTTTGCCAACGATGGCAGCATCC
TGGAGCTGTTCAAGCGGAAGATGGAGGAGGAGCAGCGGCAGCGGCAGGAGGAGCCACCCCCGGGCCCGCAGCGACCTGAT
CAACCGGCCTCCACCGCAGCGGGCCCAGGGAATCAGAAGAGGAAGGGCGGCCCAGGCCCCACGTTCAGCTTCGTGGGCAA
GCGCAGAGGCGGGAACAAACTAGCCCTCAAGACGGGAATAGTAGCCAAGAAGCAGAAGACGGAGGATGAGGTATTAACAA
GTAAAGGTGACGCGTGGGCCAAGTACATGGCAGAAGTGAAAAAGTACAAAGCCCACCAGTGCGGTGATGATGATAAAACT
CGGCCCCTGGTGAAA

Alignment

ORF - retro_rnor_1080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.09 %
• Parental protein coverage: 95.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPPGREAPGPAGSGRSRWAESGPGTSPESGDDEVSGSSPVSSGVNLFANDGSFLELFKRKMEEEQRQRQE
          EPPGREAPGPAGSGRSRWAESGPGTSPESGDDEV.GSSPVSSGVNLFANDGS.LELF.............
Retrocopy EPPGREAPGPAGSGRSRWAESGPGTSPESGDDEV*GSSPVSSGVNLFANDGSILELFXXXXXXXXXXXXX

Parental  EPPPGPQRPDQPASAAAGPGNQKRKGGPGPTFSFVGKRRGGNKLALKTGIVAKKQKTEDEVLTSKGDAWA
          ..PPGPQRPDQPAS.AAGPGNQKRKGGPGPTFSFVGKRRGGNKLALKTGIVAKKQKTEDEVLTSKGDAWA
Retrocopy XXPPGPQRPDQPASTAAGPGNQKRKGGPGPTFSFVGKRRGGNKLALKTGIVAKKQKTEDEVLTSKGDAWA

Parental  KYMAEVKKYKAHQCGDDDKTRPLVK
          KYMAEVKKYKAHQCGDDDKTRPLVK
Retrocopy KYMAEVKKYKAHQCGDDDKTRPLVK

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	7.55 RPM
SRP017611_kidney	0.07 RPM	14.17 RPM
SRP017611_liver	0.00 RPM	6.86 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1080 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1080 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1080 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000025628	1 retrocopy	retro_mdom_188,
Rattus norvegicus	ENSRNOG00000003863	3 retrocopies	retro_rnor_1080 , retro_rnor_2556, retro_rnor_2675,
Tursiops truncatus	ENSTTRG00000005460	1 retrocopy	retro_ttru_922,