RetrogeneDB ID: retro_rnor_432

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:45055885..45056687(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lims1
• Ensembl ID: ENSRNOG00000037765
• Aliases: Lims1, Pinch1, RGD1560732
• Description: LIM and senescent cell antigen-like-containing domain protein 1 [Source:RefSeq peptide;Acc:NP_001138928]

Sequence

>retro_rnor_432
AGGCAGTACTGTGAGCATGATTTCCCGATGCTCTTCGTTCCCTGCTTCCGCCAGTGTGGTGAATCCATCATTGGCTGGGT
TATCACAGCCATGAACAACAGCTGGCATCCTGAGTGCTTCCAATGCAACCTCTGCCAGGAAGTCTGGCAGACATAGGGTT
TGTCAAGAATGCTGGCAGACACTTATGTCACCCATGTCATAATTGTGAAAAGGCCAAAGGCCTTGGAAAATACATCTGCC
TGAAATGCCATGCCCTCATTAATGAACAGCCTCTGATCTTCAAGAACGACCCTTACCACCCATACCACTTCAACTGTGCC
AACCGCGGGAAGGAGCTAACTGCTGATGCTCAGGGGCTGAAAGGGGAGCTAGACTGTCTGCCAAGTCATGATAACATGGG
GATCCCTATCTGTGGTGCCTGCTAGAGGCCCATAGAAGGGCAAGTAGTGAATGCCACGGGCAAGCAATGGCCTGTGGAGT
ATTTTGTTTGTGACGAATGTGAAAAACCACTTTCTGACATCGCCATTATGAGAGGAAGGGCTTGGCCTATTGTGAAACTC
ACTGTGATCAGCTATTTGGTGATGTTTGTTTCCATTGCAACCGTGTCATAGATGGTGACGTGGTCTCTGCCCTCAACAAG
GCCTGGTGTGTGAGCTGCTTTGCCTGTCCCACCTACAATACCAAACTAACACTCAAGAATAAATTCGTGGAGATTAAGCC
AGTCTGGAAGAAATGCTCCGAGAAATGTCCTCTGGAGCTGAAGAAAAGACTTATGAAACTATCTGAGACCTTAGGAAGGA
AA

Alignment

ORF - retro_rnor_432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 74.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKYCEHDFQMLFAPCCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEV-LADIGFVKNAGRHLCRPCHNR
          R.YCEHDF.MLF.PC..QCGE.IIG.VI.AMNNSWHPECF.C.LCQEV.LADIGFVKNAGRHLC.PCHN.
Retrocopy RQYCEHDFPMLFVPCFRQCGESIIGWVITAMNNSWHPECFQCNLCQEV<LADIGFVKNAGRHLCHPCHNC

Parental  EKARGLGKYICQKCHAIIDEQPLIFKNDPYHPDHFNCANCGKELTADARELKGELYCLPCHDKMGVPICG
          EKA.GLGKYIC.KCHA.I.EQPLIFKNDPYHP.HFNCAN.GKELTADA..LKGEL.CLP.HD.MG.PICG
Retrocopy EKAKGLGKYICLKCHALINEQPLIFKNDPYHPYHFNCANRGKELTADAQGLKGELDCLPSHDNMGIPICG

Parental  ACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLG-HRHYERKGLAYCETHYNQLFGDVCFHCNRVIEGDV
          AC.RPIEG.VVNA.GKQW.VE.FVC..CEKP....HRHYERKGLAYCETH..QLFGDVCFHCNRVI.GDV
Retrocopy AC*RPIEGQVVNATGKQWPVEYFVCDECEKPLSD<HRHYERKGLAYCETHCDQLFGDVCFHCNRVIDGDV

Parental  VSALNKAWCVSCFACSTCNTKLTLKNKFVEFDMKPVCKKCYEKFPLELKKRLKKLSETLGRK
          VSALNKAWCVSCFAC.T.NTKLTLKNKFVE...KPV.KKC.EK.PLELKKRL.KLSETLGRK
Retrocopy VSALNKAWCVSCFACPTYNTKLTLKNKFVE--IKPVWKKCSEKCPLELKKRLMKLSETLGRK

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	25.81 RPM
SRP017611_kidney	0.00 RPM	37.05 RPM
SRP017611_liver	0.00 RPM	18.36 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_432 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_432 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_432 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013902	1 retrocopy	retro_chof_817,
Dasypus novemcinctus	ENSDNOG00000004334	1 retrocopy	retro_dnov_1229,
Otolemur garnettii	ENSOGAG00000001879	1 retrocopy	retro_ogar_2992,
Rattus norvegicus	ENSRNOG00000000875	1 retrocopy	retro_rnor_2514,
Rattus norvegicus	ENSRNOG00000037765	1 retrocopy	retro_rnor_432 ,