RetrogeneDB ID: retro_rnor_586

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:76948458..76949712(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Peli1
• Ensembl ID: ENSRNOG00000006329
• Aliases: None
• Description: pellino homolog 1 [Source:RefSeq peptide;Acc:NP_001094035]

Sequence

>retro_rnor_586
ATGTTTTCTCCTGATTAAGAAAATCATCCTTCCAAAGCCCCAGTAAAATATGGCGAACTCATTGTCTTAGGGTATAATGG
GTCTCTCCCAAAGGGCGACAGAGGAAGGAGGAAAAGTAGGTTTGCTTTGTTTAAAAGACCTAAGGCAAATGGGGTGAAGC
CTAGCACCGTGCACATTGCATGCACTCCTCAGGCCGCCAAGGCAATAAGCAACAAGGACCAGCATAGCATATCGTAGACT
TTATCTCGAGCCCAGACAGTGGTGGTTGAATATACTCACGACAGCAACACTGATATGTTTCAGATTGGCCGGTCAACTGA
AAGTCCTATTGATTTTGTGGTAACTGACACAGTTCCTGGAAGTCAGAGTAATTCCGACACGCAGTCCGTACAAAGCACTA
TATCGAGGTTTGCCTGTAGGATCATTTGTGAACGTAATCCTCCCTTTACAGCTCGGATTTATGCTGCAGGATTTGATTCA
TCAAAAAACATCTTTCTTGGGGAGAAGGCTACCAAATGGAAGACGTCCGACGGGCAGATGGATGGCCTGACCACTAATGG
AGTTCTTGTGATGCATCCACGCGATGGGTTCACAGAAGACTCCAAGCCTGGAATATGGAGAGAGATATCCGTATGTGGGA
ACGTCTTCAGTCTGCGTGAAACCAGATCAGCGCAACAGAGAGGAAAGATGGTGGAAATCGAAACCAATCAGCTGCAAGAT
GGCTCCTTAATCGACCTCTGTGGTGCAACCCTGCTGTGGCGCACAGCAGAAGGCCTTTCCCACACCCCTACTGTGAAACA
CTTAGAAGCTCTGAGACAGGAGATCAATGCAGCTCGGCCTCAGTGCCCTGTAGGCTTCAACACACTAGCCTTCCCCAGCA
TGAAGAGGAAAGATGTTGTAGATGAGAAGCAACCATGGGTATATGTGAACTGCGGCCATGTTCATGGTTACCATAACTGG
GGAAACAAGGAAGAACGTGACGGCAAAGATCGTGAATGTCCTATGTGTAGGTCTGTTGGTCCCTATGTCCCTCTGTGGCT
TGGATGTGAAGCTGGATTTTATGTGGACGCCGGCCCTCCCACCCATGCCTTTAGCCCCTGTGGGCATGTGTGTTCAGAAA
AGACAACGGCTTACTGGTCCCAGATCCCGCTTCCTCATGGTACGCACACTTTTCACGCAGCCTGTCCCTTCTCTGCACAT
CAGTTGGCTGGTGAACAAGGCTATATCAGACTTATTTTCCAAGGACCTCTAGAC

Alignment

ORF - retro_rnor_586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.56 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFSPDQENHPSKAPVKYGELIVLGYNGSLPNGDRGRRKSRFALFKRPKANGVKPSTVHIACTPQAAKAIS
          MFSPD.ENHPSKAPVKYGELIVLGYNGSLP.GDRGRRKSRFALFKRPKANGVKPSTVHIACTPQAAKAIS
Retrocopy MFSPD*ENHPSKAPVKYGELIVLGYNGSLPKGDRGRRKSRFALFKRPKANGVKPSTVHIACTPQAAKAIS

Parental  NKDQHSISYTLSRAQTVVVEYTHDSNTDMFQIGRSTESPIDFVVTDTVPGSQSNSDTQSVQSTISRFACR
          NKDQHSIS.TLSRAQTVVVEYTHDSNTDMFQIGRSTESPIDFVVTDTVPGSQSNSDTQSVQSTISRFACR
Retrocopy NKDQHSIS*TLSRAQTVVVEYTHDSNTDMFQIGRSTESPIDFVVTDTVPGSQSNSDTQSVQSTISRFACR

Parental  IICERNPPFTARIYAAGFDSSKNIFLGEKAAKWKTSDGQMDGLTTNGVLVMHPRDGFTEDSKPGIWREIS
          IICERNPPFTARIYAAGFDSSKNIFLGEKA.KWKTSDGQMDGLTTNGVLVMHPRDGFTEDSKPGIWREIS
Retrocopy IICERNPPFTARIYAAGFDSSKNIFLGEKATKWKTSDGQMDGLTTNGVLVMHPRDGFTEDSKPGIWREIS

Parental  VCGNVFSLRETRSAQQRGKMVEIETNQLQDGSLIDLCGATLLWRTAEGLSHTPTVKHLEALRQEINAARP
          VCGNVFSLRETRSAQQRGKMVEIETNQLQDGSLIDLCGATLLWRTAEGLSHTPTVKHLEALRQEINAARP
Retrocopy VCGNVFSLRETRSAQQRGKMVEIETNQLQDGSLIDLCGATLLWRTAEGLSHTPTVKHLEALRQEINAARP

Parental  QCPVGFNTLAFPSMKRKDVVDEKQPWVYLNCGHVHGYHNWGNKEERDGKDRECPMCRSVGPYVPLWLGCE
          QCPVGFNTLAFPSMKRKDVVDEKQPWVY.NCGHVHGYHNWGNKEERDGKDRECPMCRSVGPYVPLWLGCE
Retrocopy QCPVGFNTLAFPSMKRKDVVDEKQPWVYVNCGHVHGYHNWGNKEERDGKDRECPMCRSVGPYVPLWLGCE

Parental  AGFYVDAGPPTHAFSPCGHVCSEKTTAYWSQIPLPHGTHTFHAACPFCAHQLAGEQGYIRLIFQGPLD
          AGFYVDAGPPTHAFSPCGHVCSEKTTAYWSQIPLPHGTHTFHAACPF.AHQLAGEQGYIRLIFQGPLD
Retrocopy AGFYVDAGPPTHAFSPCGHVCSEKTTAYWSQIPLPHGTHTFHAACPFSAHQLAGEQGYIRLIFQGPLD

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	0.29 RPM	12.94 RPM
SRP017611_kidney	0.07 RPM	9.35 RPM
SRP017611_liver	0.00 RPM	5.11 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_586 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_586 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_586 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000009443	1 retrocopy	retro_cpor_306,
Rattus norvegicus	ENSRNOG00000006329	1 retrocopy	retro_rnor_586 ,