RetrogeneDB ID: retro_rnor_519

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:205799196..205799853(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Prkacb
• Ensembl ID: ENSRNOG00000004978
• Aliases: None
• Description: cAMP-dependent protein kinase catalytic subunit beta [Source:UniProtKB/Swiss-Prot;Acc:P68182]

Sequence

>retro_rnor_519
AAAGAATTCCTAGCCAAAGCCAAAGAAGACTTTCTGAGGAAATGGGAGAACCCTCCCCCGAGTAATGCTGGGCTTGAGGA
TTTTGAAAGGAAAAAAACCCTTGGAACGGGTTCCTTCGGAAGAGTCATGCTGGTAAAGCATAAAGCCACTGCACAGTACT
ACGCCATGAAGATCTTAGACAAGCAGAAGGTCGTTAAGCTAAAGCAAATAGAGCACACTCTGAATGAGAAGAGAATCCTG
CAGGCAGTGGAGTTCCCGTTCCTTGTTCGGCTGGAGTATTCTTTTAAGGATAATTCTAATTTATACATGGTTATGGAATA
CGTTCCTGGGGGGGAAATGTTTTCACATCTAAGAAGAATTGGAAGGTTCAGTGAACCCCATGCTCGTTTCTATGCAGCTC
AGATCGTGCTAACATTTGAGTACCTCCATTCCCTCGACCTCATCTACAGAGATCTCAAGCCGGAAAACCTCTTAATTGAC
CACCAGGGTTACATCCAGGTCACAGATTTTGGGTTCGCCAAGAGAGTCAAGGGCAGGACTTGGACATTGTGTGGCACCCC
AGAGTACCTGGCCCCAAAGATCATCCTCAGCAAGGGTTACAATAAGGCAGTGGACTGGTGGGCATTGGGTGTACTGATCT
ACGAGATGGCTGCTGGC

Alignment

ORF - retro_rnor_519 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.09 %
• Parental protein coverage: 62.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEFLAKAKEDFLRKWENPPPSNAGLEDFERKKTLGTGSFGRVMLVKHKATEQYYAMKILDKQKVVKLKQI
          KEFLAKAKEDFLRKWENPPPSNAGLEDFERKKTLGTGSFGRVMLVKHKAT.QYYAMKILDKQKVVKLKQI
Retrocopy KEFLAKAKEDFLRKWENPPPSNAGLEDFERKKTLGTGSFGRVMLVKHKATAQYYAMKILDKQKVVKLKQI

Parental  EHTLNEKRILQAVEFPFLVRLEYSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFE
          EHTLNEKRILQAVEFPFLVRLEYSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFE
Retrocopy EHTLNEKRILQAVEFPFLVRLEYSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFE

Parental  YLHSLDLIYRDLKPENLLIDHQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALG
          YLHSLDLIYRDLKPENLLIDHQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAP.IILSKGYNKAVDWWALG
Retrocopy YLHSLDLIYRDLKPENLLIDHQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPKIILSKGYNKAVDWWALG

Parental  VLIYEMAAG
          VLIYEMAAG
Retrocopy VLIYEMAAG

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	0.50 RPM	88.43 RPM
SRP017611_kidney	0.14 RPM	17.45 RPM
SRP017611_liver	0.07 RPM	6.45 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_519 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_519 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_519 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000003457	1 retrocopy	retro_mmul_186,
Nomascus leucogenys	ENSNLEG00000009888	1 retrocopy	retro_nleu_2469,
Pongo abelii	ENSPPYG00000001209	1 retrocopy	retro_pabe_61,
Rattus norvegicus	ENSRNOG00000004978	1 retrocopy	retro_rnor_519 ,
Tarsius syrichta	ENSTSYG00000000380	2 retrocopies	retro_tsyr_1640, retro_tsyr_1802,