RetrogeneDB ID: retro_rnor_2299

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:74550783..74551490(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gpatch4
• Ensembl ID: ENSRNOG00000018969
• Aliases: Gpatch4, RGD1311086
• Description: G patch domain-containing protein 4 [Source:UniProtKB/Swiss-Prot;Acc:Q566R3]

Sequence

>retro_rnor_2299
ATGAGTGTTGCCCCAGAGGTTAAGAGTCATGGGATGAAGTTTGCTGAAGAGCAGCTGCTGAAGCATTCATGGACTCAAGG
CAAAGGCCTGGGCTGGAAGGAGAATGGCATCACCCAGGCCCTTAAGGTGACACTGAAACAAGACACCCATGTGGTGGGAC
ATGCCCTTGCCAAGGAGTTTCCAAACCAGTGGTAAAGTGATCTCTTAACAAGACTACTGTCAACTTGGTAATGGACTCAG
GCAAGGATGGAGTGCAGATAAGGCATCTTTCCAAGGAGACCACACAGTGCTATCACTCCATGCTCAGCTTGCTGTATCAG
AAGTTTGTGAAGACAGACGCACTAACCTCAGGTGAAAAGAAGTCTGGCAGAGACTTGGGGAGCTGCAGTGATGTTGATAA
CCATGAATCCATGCCCCCAAAGATTCTGACTGATGAGATGCTACCCAAAGCTTGTGAGAGGTAACAGCACACAAGGCTGC
CAAGATTGGAGTCACCATGAAAGCCAAGCTTGTTTGCCTGGAAGCTCAAGAGCAGTTCTGCCTGGCTTAGCTCAAAGGCT
CTAAGGACGTGGGTACTTCTCAACCACTGACTGATAGCAAGCCCTCCCAAAAAAAGAAAAAGAAGAGGAAGCAGAAAGAG
GAGGAAGAGGCTGCAACAACTGAAGAGTCTAGGTGAAGAGCTCCTGAAACACACTGACAAGAGCTTC

Alignment

ORF - retro_rnor_2299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.92 %
• Parental protein coverage: 58.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSVTPEVKSRGMKFAEEQLLKHGWTQGKGLGRKENGITQALKVTLKQDTHGVGHDPAKEFTDHWWSDLF-
          MSV.PEVKS.GMKFAEEQLLKH.WTQGKGLG.KENGITQALKVTLKQDTH.VGH..AKEF...W.SDL..
Retrocopy MSVAPEVKSHGMKFAEEQLLKHSWTQGKGLGWKENGITQALKVTLKQDTHVVGHALAKEFPNQW*SDLL<

Parental  NKTAANLVVDSGKDGVQIRRLSKETTQRSHSKPSLLYQKFVKTATLTSGEEKPDRDLESCSDVDNREPIP
          NKT..NLV.DSGKDGVQIR.LSKETTQ..HS..SLLYQKFVKT..LTSGE.K..RDL.SCSDVDN.E..P
Retrocopy NKTTVNLVMDSGKDGVQIRHLSKETTQCYHSMLSLLYQKFVKTDALTSGEKKSGRDLGSCSDVDNHESMP

Parental  PKILTDEMLLKACEG-RTAHKAARIGITMKAKLARLEAQEQAFLARLKGSKDVGTSQPLTDSEPSQKKKK
          PKILTDEML.KACE...TAHKAA.IG.TMKAKL..LEAQEQ..LA.LKGSKDVGTSQPLTDS.PS.....
Retrocopy PKILTDEMLPKACER<VTAHKAAKIGVTMKAKLVCLEAQEQFCLA*LKGSKDVGTSQPLTDSKPSXXXXX

Parental  RRKQKEEEEAATTE-KSLGEELLEHTDKSF
          .RKQKEEEE.A.T..KSLGEELL.HTDKSF
Retrocopy KRKQKEEEE-AATT>KSLGEELLKHTDKSF

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	12.22 RPM
SRP017611_kidney	0.00 RPM	3.70 RPM
SRP017611_liver	0.00 RPM	3.09 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2299 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2299 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2299 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000013624	2 retrocopies	retro_mmur_1516, retro_mmur_63,
Otolemur garnettii	ENSOGAG00000006698	1 retrocopy	retro_ogar_2053,
Rattus norvegicus	ENSRNOG00000018969	1 retrocopy	retro_rnor_2299 ,