RetrogeneDB ID: retro_rnor_683

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:40728102..40728568(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Uxt
• Ensembl ID: ENSRNOG00000009893
• Aliases: None
• Description: Protein UXT [Source:UniProtKB/Swiss-Prot;Acc:Q63ZY7]

Sequence

>retro_rnor_683
ATGGTGATGACCCCCAAACAATGGGCCTTAGGTACTACAGGTGAGAAAGTGCTGTGGTCGAGGCCTTTATCAGTGATGTT
TTGCAGTGAGACTTGCAGAAGGCACTGGACCATTGGGACTTAGGTATATGACAGCTGTTCTTATACCTTCAACTGAGAAA
TGTCATTGAGTCATTCCAGGAACCTATTTACTCAGAGTTATATGTGCGGGTGGATTTGGGCTGTAACTTCTTCATTGTCA
CAGCGGTCCCAGATCTTTCACATATCTGTGTGTCTCTGGGATATGGCTTTTTCCTGGAGTTGATACTGGCTGAAGTTCTC
AAGTTCATTGACTGAAAGAGCTCTCTCCTCACAGAGCTCAGGATCTTCCTCATCAAGGACTCTATGAATATAAGGCCCAG
ATCCTCACCGTGGTGGGAGGACATAGAGAAGTACGAGGCCTGCAGAACTTCCCAGAGCCATGTCCC

Alignment

ORF - retro_rnor_683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.72 %
• Parental protein coverage: 99.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATPPKRRALDTVGEKVLR-YEAFISDVLQRDLQKVLDHRDKVYEQLSVYLQLRNVIERLQETNHSELYM
          M...PK..AL.T.GEKVL...EAFISDVLQ.DLQK.LDH.D....QL..YLQLRNVIE..QE...SELY.
Retrocopy MVMTPKQWALGTTGEKVLW<VEAFISDVLQ*DLQKALDHWDLGI*QLFLYLQLRNVIESFQEPIYSELYV

Parental  QVDLGCNFFVDTMVPDTSRIYVALGYGFFLELTLAEALKFIDRKSSLLTELSDSLTKDSMNI-KANIHMM
          .VDLGCNFF..T.VPD.S.I.V.LGYGFFLEL.LAE.LKFID.KSSLLTEL...L.KDSMNI.KA.I...
Retrocopy RVDLGCNFFIVTAVPDLSHICVSLGYGFFLELILAEVLKFID*KSSLLTELRIFLIKDSMNI<KAQILTV

Parental  LEGLRELQGLQNFPEPSP
          ..G.RE..GLQNFPEP.P
Retrocopy VGGHREVRGLQNFPEPCP

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	9.27 RPM
SRP017611_kidney	0.00 RPM	16.96 RPM
SRP017611_liver	0.00 RPM	10.69 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_683 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_683 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_683 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_715

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000009154	1 retrocopy	retro_cpor_1302,
Dipodomys ordii	ENSDORG00000001025	1 retrocopy	retro_dord_627,
Erinaceus europaeus	ENSEEUG00000006151	1 retrocopy	retro_eeur_543,
Macropus eugenii	ENSMEUG00000003352	1 retrocopy	retro_meug_59,
Microcebus murinus	ENSMICG00000016263	1 retrocopy	retro_mmur_1156,
Mustela putorius furo	ENSMPUG00000013405	1 retrocopy	retro_mputfur_999,
Mus musculus	ENSMUSG00000001134	3 retrocopies	retro_mmus_1424, retro_mmus_1766, retro_mmus_715,
Rattus norvegicus	ENSRNOG00000009893	5 retrocopies	retro_rnor_521, retro_rnor_522, retro_rnor_683 , retro_rnor_692, retro_rnor_882,
Tarsius syrichta	ENSTSYG00000012719	2 retrocopies	retro_tsyr_237, retro_tsyr_778,