RetrogeneDB ID: retro_rnor_1139

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:22981000..22981863(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000009874
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rfc5
• Ensembl ID: ENSRNOG00000001134
• Aliases: None
• Description: replication factor C subunit 5 [Source:RefSeq peptide;Acc:NP_001100616]

Sequence

>retro_rnor_1139
TTCATCAGTGAAGACCGCCTACCACACCTACTTCTCTATGGCCCTCCAGGCACAGGAAAGACATCCACCATCCTGGCCTG
GGCCAAACAACTTTACAAAGGTAAAGAATTCGGCTCCATGGTCTTGGAGCTGAATGCTTCCGACAACCGAGGAATCGATA
TCGTTCGGGGGCCAGTCCTCAGCTTTGCCAACACAAGGACAATCTTCAAGAGAGGGTTTAAGCTTCTGATCCTGGACGAA
GCTGACGCCATGACTCAAGATGCCCAGATGCCTTAAAACGAGTGATTGAGAAGTTCACGGAAAACACCAGGTTTTGCCTC
ATCTGTAACTACCTGTCCAAGATCATCCCTGCCTTGCAGTCACGGTACATGAGGTTCCGATTTGGCCCTCTGAGACTCGA
GCTCATGGTTCCTCAACTGGAACATGTAGTACAAGAAGAGAACGTGGATATGAGTGAGGATGCAATGAAGGCTCTTGTCA
CTCTGTCCAGTGGGGACATGCGAAGGGCTTTGAACATTATGCAGAGTACCAATACGGCCTTTGGGAAGGTGACAGAGGAG
ACTTGTCTACACCTGCAACGGAAACCCACTCAAGACGGACATTGCCAACATTCTGGACTGGATGCTGAATCAAGACTTCA
TCACTGCCTAAAAAATACCATGGAGCTGAAGACCCTGAAGAGTGTGGCACTGCGTGACATCCTGACAGAGGTTCACTTGT
TTGTGCATGGAGTTGACTTTCCATATTCAGATCGGATACATTTATTGACCAAAATGACAGACACTGAGTGCAGACTTTCT
GTTGGCACCAGTCAGAAGACACAGCTGTTCTCCCTCATTGCTGCTTTTCAAGTTACCAGAGAG

Alignment

ORF - retro_rnor_1139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.6 %
• Parental protein coverage: 85.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FISEDRLPHLLLYGPPGTGKTSTILACAKQLYKDKEFGSMVLELNASDDRGIDIVRGPILSFASTRTIFK
          FISEDRLPHLLLYGPPGTGKTSTILA.AKQLYK.KEFGSMVLELNASD.RGIDIVRGP.LSFA.TRTIFK
Retrocopy FISEDRLPHLLLYGPPGTGKTSTILAWAKQLYKGKEFGSMVLELNASDNRGIDIVRGPVLSFANTRTIFK

Parental  RGFKLVILDEADAMTQDAQ-NALRRVIEKFTENTRFCLICNYLSKIIPALQSRCTRFRFGPLTPELMVPR
          RGFKL.ILDEADAMTQDAQ..AL.RVIEKFTENTRFCLICNYLSKIIPALQSR..RFRFGPL..ELMVP.
Retrocopy RGFKLLILDEADAMTQDAQ<DALKRVIEKFTENTRFCLICNYLSKIIPALQSRYMRFRFGPLRLELMVPQ

Parental  LEHVVQEENVDISEDGMKALVTLSSGDMRRALNILQSTNMAFGKVTEET-VYTCTGHPLKTDIANILDWM
          LEHVVQEENVD.SED.MKALVTLSSGDMRRALNI.QSTN.AFGKVTEET.VYTC.G.PLKTDIANILDWM
Retrocopy LEHVVQEENVDMSEDAMKALVTLSSGDMRRALNIMQSTNTAFGKVTEET>VYTCNGNPLKTDIANILDWM

Parental  LNQDFTTA-YKNIMELKTLKGLALHDILTEVHLFVHRVDFPSSVRMHLLTKMADIEYRLSVGTSEKIQLS
          LNQDF.TA..KN.MELKTLK..AL.DILTEVHLFVH.VDFP.S.R.HLLTKM.D.E.RLSVGTS.K.QL.
Retrocopy LNQDFITA<LKNTMELKTLKSVALRDILTEVHLFVHGVDFPYSDRIHLLTKMTDTECRLSVGTSQKTQLF

Parental  SLIAAFQVTRD
          SLIAAFQVTR.
Retrocopy SLIAAFQVTRE

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	0.07 RPM	11.00 RPM
SRP017611_kidney	0.00 RPM	9.77 RPM
SRP017611_liver	0.00 RPM	4.30 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1139 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1139 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015326	2 retrocopies	retro_ecab_613, retro_ecab_946,
Mus musculus	ENSMUSG00000029363	1 retrocopy	retro_mmus_2495,
Oryctolagus cuniculus	ENSOCUG00000010377	1 retrocopy	retro_ocun_1316,
Rattus norvegicus	ENSRNOG00000001134	1 retrocopy	retro_rnor_1139 ,