RetrogeneDB ID: retro_rnor_48

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: AABR06111133.1:2..986(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000049840
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Acp5
• Ensembl ID: ENSRNOG00000046261
• Aliases: Acp5, TTRRAP, Trap
• Description: Tartrate-resistant acid phosphatase type 5 [Source:UniProtKB/Swiss-Prot;Acc:P29288]

Sequence

>retro_rnor_48
ATGGATTCATGGGTGGTGCTGCTGGGCCTACAAATCATATGGCTCCCACTCCTGACCCACGGTACAGCCCCCACTCCCAC
CCTGAGATTTGTGGCTGTGGGCGACTGGGGAGGGGTCCCCAATGCCCCATTCCACACAGCCCGGGAAATGGCCAATGCCA
AAGAGATCGCCAGAACCGTGCAGACGATGGGCGCTGACTTCATCATGTCTCTGGGGGACAATTTCTACTTCACTGGAGTG
CACGATGCCAGCGACAAGAGGTTCCAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTTCGCAACATCCCCTGGTA
TGTGCTGGCTGGAAACCATGATCACCTTGGCAACGTCTCTGCACAGATTGCATACTCTAAGATCTCCAAGCGCTGGAACT
TCCCCAGCCCTTACTACCGTTTGCGCTTCAAAATTCCACGTACAAACATAACTGTGGCCATCTTTATGCTGGACACAGTG
ATGCTGTGTGGCAACTCAGATGACTTTGCCAGTCAGCAGCCCAAAATGCCTCGAGACCTGGGAGTGGCCCGCACTCAGCT
GTCCTGGCTCAAAAAGCAGTTGGCAGCAGCCAAGGAGGACTACGTTTTGGTGGCCGGCCACTACCCCATCTGGTCCATCG
CCGAGCACGGACCCACGCGCTGCCTTGTCAAGAACTTGCGACCATTGTTAGCCACATACGGGGTCACTGCCTACCTGTGT
GGACATGACCACAACCTGCAGTATCTTCAGGACGAGAACGGTGTGGGCTATGTGCTGAGTGGGGCCGGCAACTTCATGGA
TCCCTCTGTGCGACATCAACGAAAGGTCCCCAACGGCTACTTGCGGTTTCACTATGGATCTGAGGACTCCCTGGGCGGCT
TCACACATGTGGAGATAAGCCCCAAAGAAATGACCATCATATATGTGGAAGCCTCTGGAAAATCACTCTTTAAGACCAGC
CTCCCAAGGAGACCCAGACCCTGA

Alignment

ORF - retro_rnor_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.88 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTWMVLLGLQILLLPLLAHCTAPASTLRFVAVGDWGGVPNAPFHTAREMANAKEIARTVQIMGADFIMS
          MD.W.VLLGLQI..LPLL.H.TAP..TLRFVAVGDWGGVPNAPFHTAREMANAKEIARTVQ.MGADFIMS
Retrocopy MDSWVVLLGLQIIWLPLLTHGTAPTPTLRFVAVGDWGGVPNAPFHTAREMANAKEIARTVQTMGADFIMS

Parental  LGDNFYFTGVHDANDKRFQETFEDVFSDRALRNIPWYVLAGNHDHLGNVSAQIAYSKISKRWNFPSPYYR
          LGDNFYFTGVHDA.DKRFQETFEDVFSDRALRNIPWYVLAGNHDHLGNVSAQIAYSKISKRWNFPSPYYR
Retrocopy LGDNFYFTGVHDASDKRFQETFEDVFSDRALRNIPWYVLAGNHDHLGNVSAQIAYSKISKRWNFPSPYYR

Parental  LRFKVPRSNITVAIFMLDTVMLCGNSDDFVSQQPEMPRDLGVARTQLSWLKKQLAAAKEDYVLVAGHYPI
          LRFK.PR.NITVAIFMLDTVMLCGNSDDF.SQQP.MPRDLGVARTQLSWLKKQLAAAKEDYVLVAGHYPI
Retrocopy LRFKIPRTNITVAIFMLDTVMLCGNSDDFASQQPKMPRDLGVARTQLSWLKKQLAAAKEDYVLVAGHYPI

Parental  WSIAEHGPTRCLVKNLRPLLAAYGVTAYLCGHDHNLQYLQDENGVGYVLSGAGNFMDPSVRHQRKVPNGY
          WSIAEHGPTRCLVKNLRPLLA.YGVTAYLCGHDHNLQYLQDENGVGYVLSGAGNFMDPSVRHQRKVPNGY
Retrocopy WSIAEHGPTRCLVKNLRPLLATYGVTAYLCGHDHNLQYLQDENGVGYVLSGAGNFMDPSVRHQRKVPNGY

Parental  LRFHYGSEDSLGGFTYVEIGSKEMSITYVEASGKSLFKTSLPRRPRP
          LRFHYGSEDSLGGFT.VEI..KEM.I.YVEASGKSLFKTSLPRRPRP
Retrocopy LRFHYGSEDSLGGFTHVEISPKEMTIIYVEASGKSLFKTSLPRRPRP

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	1.80 RPM
SRP017611_kidney	0.00 RPM	49.68 RPM
SRP017611_liver	0.00 RPM	8.07 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_48 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_48 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_48 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000046261	1 retrocopy	retro_rnor_48 ,