RetrogeneDB ID: retro_rnor_1838

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:152612848..152613283(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000048732
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Utp11l
• Ensembl ID: ENSRNOG00000007174
• Aliases: Utp11l, Cgi-94, Cgi94, RGD1559610
• Description: probable U3 small nucleolar RNA-associated protein 11 [Source:RefSeq peptide;Acc:NP_001101448]

Sequence

>retro_rnor_1838
TTTCACAAGGCAGCCCAGACTCAGCAGCGAGAACACCGAGAACGAAGCAAGCCTGTTTTTCTAAAAATGCCTGGGTTAGC
TGAAGAAAAAGAAAAATTACAAACTTCATGCAAATGGCTATCGTCAAAAAACAGGAATTTCTCAGAGCTCTCTGGAAGGG
TCTTGAAAAAAAGTCCAGATGAATTCTACAATAAAATGACTCAGGCCGAGGTCCAGGATGGAGACCACACTTTCAAAGAG
AGCAAGGAAGAAGGAACAGCAGGGCAGCTAAAGCTGGTGAGAAGTCAGGACATCAGTACATAGAGATGAAAGGGGTTGCA
GAAGCAAAGACAATTGAAAGACTGAAACCAGAGCGCCGTCTGCTGGATTTACAGGGGAAGCAACAAAATAAGCATATGTT
GTGTTTTTGACACCAAAAAGAAAGTTGGACAGTTT

Alignment

ORF - retro_rnor_1838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.67 %
• Parental protein coverage: 57.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FRKAAKTRQREHRERSQPGFRKRLGL-LEKKKDYKLRANDYH-KKQDFLRALRKKALE-KNPDEFYYKMT
          F.KAA.T.QREHRERS.P.F.K..GL.L.KKK.YKL.AN.Y..KKQ.FLRAL..K.LE.K.PDEFY.KMT
Retrocopy FHKAAQTQQREHRERSKPVFLKMPGL>LKKKKNYKLHANGYR>KKQEFLRAL-WKGLE>KSPDEFYNKMT

Parental  RAKLQDGVHIFKDNKEEVTAEQLKLMRTQDI-KYIEMKRVAEAKKIERLKSELHLLDVQGKQQNKHVF-F
          .A..QDG.H.FK..KEE.TA.QLKL.R.QDI..YIEMK.VAEAK.IERLK.E..LLD.QGKQQNKH....
Retrocopy QAEVQDGDHTFKESKEEGTAGQLKLVRSQDI<QYIEMKGVAEAKTIERLKPERRLLDLQGKQQNKHML>V

Parental  FDTKKEVEQF
          FDTKK.V.QF
Retrocopy FDTKKKVGQF

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	16.90 RPM
SRP017611_kidney	0.00 RPM	19.75 RPM
SRP017611_liver	0.00 RPM	10.15 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1838 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1838 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1838 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001043	1 retrocopy	retro_cpor_1084,
Microcebus murinus	ENSMICG00000001496	1 retrocopy	retro_mmur_894,
Myotis lucifugus	ENSMLUG00000001003	1 retrocopy	retro_mluc_2386,
Mus musculus	ENSMUSG00000028907	1 retrocopy	retro_mmus_1968,
Oryctolagus cuniculus	ENSOCUG00000007154	2 retrocopies	retro_ocun_1285, retro_ocun_669,
Otolemur garnettii	ENSOGAG00000016492	2 retrocopies	retro_ogar_3229, retro_ogar_3324,
Rattus norvegicus	ENSRNOG00000007174	1 retrocopy	retro_rnor_1838 ,