RetrogeneDB ID: retro_rnor_2888

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:3480054..3480475(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gins1
• Ensembl ID: ENSRNOG00000008091
• Aliases: Gins1, RGD1562246
• Description: GINS complex subunit 1 [Source:RefSeq peptide;Acc:NP_001102677]

Sequence

>retro_rnor_2888
CCCCAAAGGCAGCTTCCAGCCTTCAAGGAAAATGCACTGAGGCATGTTCTGGAGGAGTTGAAAACTTTATATGAACAGAA
CAAGTCTGATGTGAATTAAGCAAAGCTACCTGGATGAGATGATCTGATACCAACCAGCAAATTTTGGCATTGGTTAACAA
ATGGAGTCTTCACTATAGCATTCTGCACTCTGCACTTAGGCCAGGTGCTTTGAATTAGAGCACTCAGGTGGGAATGTGGG
AGCATCTTGCTAAGTGCTTTACAGTTCCACACATATGCTGAAGAAATAGGCTGGTTCAACCATTATAAAATGTCTCTTGC
TACTTACATGAGGCCACTGGGAGGAGACAAAGGTTTACATATCACACAGGATGTGAAACTTCCAAAACCACTAATATATT
AGAGTATAGTGTCTAAAAGAC

Alignment

ORF - retro_rnor_2888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 70.92 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PEGQLPAFNEDGLRQVLEEMKALYEQNQSDVNEAKSAGRGDLIPTIKFRHCSLLRNRRCTIAYL---YDR
          P..QLPAF.E..LR.VLEE.K.LYEQN.SDVN.AK..G..DLIPT.KF.H...L.N...TIA........
Retrocopy PQRQLPAFKENALRHVLEELKTLYEQNKSDVN*AKLPG*DDLIPTSKFWHW--LTNGVFTIAFCTLHLGQ

Parental  LLRIRALRWEYGSVLPNPLRFHMSAEEVEWFNHYKKSLATYMRSLGGDEGLDITQDVKPPKSL-YIEVRC
          .L.IRALRWE.GS.L...L.FH..AEE..WFNHYK.SLATYMR.LGGD.GL.ITQDVK.PK.L.YI.V.C
Retrocopy VL*IRALRWECGSILLSALQFHTYAEEIGWFNHYKMSLATYMRPLGGDKGLHITQDVKLPKPL>YIRV*C

Parental  LKD
          LKD
Retrocopy LKD

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	0.65 RPM
SRP017611_kidney	0.00 RPM	0.70 RPM
SRP017611_liver	0.00 RPM	0.27 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2888 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2888 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2888 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002718	1 retrocopy	retro_etel_1594,
Macropus eugenii	ENSMEUG00000016481	1 retrocopy	retro_meug_1309,
Monodelphis domestica	ENSMODG00000006443	1 retrocopy	retro_mdom_1191,
Rattus norvegicus	ENSRNOG00000008091	1 retrocopy	retro_rnor_2888 ,
Sarcophilus harrisii	ENSSHAG00000017422	1 retrocopy	retro_shar_343,
Sus scrofa	ENSSSCG00000024720	1 retrocopy	retro_sscr_238,