RetrogeneDB ID: retro_rnor_2514

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:26271639..26272479(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000006998
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fhl1
• Ensembl ID: ENSRNOG00000000875
• Aliases: Fhl1, SLIM1
• Description: Four and a half LIM domains protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9WUH4]

Sequence

>retro_rnor_2514
ACCATGTCTGAGTTCAAATGCCACCATTGCCGGGAATCCTTGCAAGGTAAAAAGTATGTGCAGAAGGATAACTTCAACTA
CTGCGTGACATGCTTTGATGCACACTGTGCCAATATCTGTGTGGAATGCAACAAGCCCATAGGTGCAGACTCCAAGGAGG
TGTGTTATAAGGAGCGATTCTGGCACAACACCTGCTTCAAATGTTCCAAGTGCCTTCAACCCTTGGCTACTGAGACCTTT
GTGGTCTGGGACAACAAGATCCTGTGCAATAATTGTGTCAGTCAACAGGCCTTCCCCAAGTGCAAAGGGTGCCTCAAGGA
TATTAAGCAAGGAGAGCAGAGTGTGGAATACAAAGGTACCATCTGGCATAAAGACTGCTTTGTCTGCAGCAACTGCAAGG
AAGTCATTGGAACCAAAACTTTCTTCCCTAAAGATGAGGGATTCTACTGTGTGGCTTGCTATGACATCTTGTTTACCAAG
TATTGTGTGAAATGCAACAAGCCCATCACATCTGGAGGAGTCAGTTACCAGGATCAGCCCTGGCATAGTGAGTGCTTTGT
ATGTGTTAACTGCTCTAAGGAGCTGAGTGAACAGCGTTTCACTGTTATGGATGACAAGATTTTTTGCGTGGATTGCTACA
AGAACTTTATAGCCAAGAAGTGTGCTGGGTGCAAGAACCCCATCACTGGGTTTGGTAAAGGCTCCAATGTGGTGACCCAC
GAGACAAATTCCTGGCATGACTACTGCTTCAACTGCAAAGCCTGTTCTGTAAATCTAGCCAATAAGCACTTTGTGTTTCA
TCAAGAGCAGATATACTGTCCTGACTGTGCCAAAAAGCTA

Alignment

ORF - retro_rnor_2514 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.53 %
• Parental protein coverage: 94.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TMSEKFDCHYCRDPLQGKKYVQKDGRHCCLKCFDKFCANTCVECRKPISADAKEVHYKNRYWHDTCFRCA
          TMSE.F.CH.CR..LQGKKYVQKD....C..CFD..CAN.CVEC.KPI.AD.KEV.YK.R.WH.TCF.C.
Retrocopy TMSE-FKCHHCRESLQGKKYVQKDNFNYCVTCFDAHCANICVECNKPIGADSKEVCYKERFWHNTCFKCS

Parental  KCLHPLASETFVSKDGKILCNKCATREDSPRCKGCFKAIVAGDQNVEYKGTIWHKDCFTCSNCKQVIGTG
          KCL.PLA.ETFV..D.KILCN.C......P.CKGC.K.I..G.Q.VEYKGTIWHKDCF.CSNCK.VIGT.
Retrocopy KCLQPLATETFVVWDNKILCNNCVSQQAFPKCKGCLKDIKQGEQSVEYKGTIWHKDCFVCSNCKEVIGTK

Parental  SFFPKGEDFYCVTCHETKFAKHCVKCNKAITSGGITYQDQPWHAECFVCVTCSKKLAGQRFTAVEDQYYC
          .FFPK.E.FYCV.C....F.K.CVKCNK.ITSGG..YQDQPWH.ECFVCV.CSK.L..QRFT...D...C
Retrocopy TFFPKDEGFYCVACYDILFTKYCVKCNKPITSGGVSYQDQPWHSECFVCVNCSKELSEQRFTVMDDKIFC

Parental  VDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHNEQVYCPDCAKK
          VDCYKNF.AKKCAGCKNPITGFGKGS.VV..E..SWHDYCF.CK.CSVNLANK.FVFH.EQ.YCPDCAKK
Retrocopy VDCYKNFIAKKCAGCKNPITGFGKGSNVVTHETNSWHDYCFNCKACSVNLANKHFVFHQEQIYCPDCAKK

Parental  L
          L
Retrocopy L

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	0.58 RPM	75.63 RPM
SRP017611_kidney	0.35 RPM	38.66 RPM
SRP017611_liver	0.07 RPM	3.90 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2514 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2514 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2514 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000014336	2 retrocopies	retro_mluc_311, retro_mluc_814,
Mus musculus	ENSMUSG00000023092	1 retrocopy	retro_mmus_51,
Nomascus leucogenys	ENSNLEG00000002560	1 retrocopy	retro_nleu_618,
Rattus norvegicus	ENSRNOG00000000875	1 retrocopy	retro_rnor_2514 ,
Rattus norvegicus	ENSRNOG00000037765	1 retrocopy	retro_rnor_432,