RetrogeneDB ID: retro_rnor_2326

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:130816217..130816693(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pqbp1
• Ensembl ID: ENSRNOG00000007766
• Aliases: None
• Description: polyglutamine-binding protein 1 [Source:RefSeq peptide;Acc:NP_001013979]

Sequence

>retro_rnor_2326
CCTGTTGCACTGCAGACCCCGGCTAGGTATAAAGGAACATCCAAACATCTGGAGCCAGAGCCAGAGGAGGAGATTATCGC
TGAAGACAACGATGATGATGCTGTTGACTATGAGACCACTCAGACAGCGGGCCTGCCACCGAGCTGTTACAAAGTGTTTG
ACCTTTCTTGTGGACTCCCTTGCTACCGGAATGTGGAGAAAGATCTCTTCTTGTCCTGGCTTTCTTCACATGATCATACC
TTTGTTGTTACCAAATCTGCCAAGAAATTCAGGAACAATAATGCAGATGCTAAGGACAAGTTGGACCGGAATCATGAGAC
GCTGAACAGAAATCAAGAGAAATCAGATCTTCTGTCACGAGAAGCCAGACAGGAGCCAAGACAAGGCAGATCAAAACCAG
GATAAGTTTGACCCAAAAAAGAGAGCATAACGTTGAGAAAGTGGAGAGGGAGGGAGGGACGCAAGGACAGAGGGAG

Alignment

ORF - retro_rnor_2326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.0 %
• Parental protein coverage: 59.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVALQTRLAKRGILKHLEPEPEEEIIAEDYDDDPVDYEATRIEGLPPSWYKVFDPSCGLPYYWNVETDL-
          PVALQT.....G..KHLEPEPEEEIIAED.DDD.VDYE.T...GLPPS.YKVFD.SCGLP.Y.NVE.DL.
Retrocopy PVALQTPARYKGTSKHLEPEPEEEIIAEDNDDDAVDYETTQTAGLPPSCYKVFDLSCGLPCYRNVEKDLF

Parental  VSWLSPHDPNFVVSKSAKKLRNSNADAEDKSERNLEKVDRNHEKSDR-SHEKPDRSHEKADRNHEKSD-R
          .SWLS.HD..FVV.KSAKK.RN.NADA.DK..RN.E...RN.EKSD...HEKPDRS..KAD.N..K.D..
Retrocopy LSWLSSHDHTFVVTKSAKKFRNNNADAKDKLDRNHETLNRNQEKSDL>CHEKPDRSQDKADQNQDKFD>Q

Parental  ERERNYDKVDRERDRDRERE
          .RE.N..KV.RE......RE
Retrocopy KREHNVEKVEREGGTQGQRE

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	22.86 RPM
SRP017611_kidney	0.00 RPM	15.00 RPM
SRP017611_liver	0.00 RPM	5.98 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2326 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2326 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2326 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_891

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000004165	2 retrocopies	retro_meug_1293, retro_meug_435,
Mus musculus	ENSMUSG00000031157	1 retrocopy	retro_mmus_891,
Rattus norvegicus	ENSRNOG00000007766	1 retrocopy	retro_rnor_2326 ,
Tupaia belangeri	ENSTBEG00000008669	1 retrocopy	retro_tbel_1908,