RetrogeneDB ID: retro_rnor_424

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:19850106..19851003(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ruvbl1
• Ensembl ID: ENSRNOG00000013195
• Aliases: Ruvbl1, NMP238, Pontin52, Tip49a
• Description: RuvB-like 1 [Source:UniProtKB/Swiss-Prot;Acc:P60123]

Sequence

>retro_rnor_424
ATGAAGATTGAGGAGGTGAAGAGCACCACGATGATGCAGCACATCGCCTCCCATAGTCACATGAAAGGTCTTGGGCTGGA
CGATAGACGCCTGGCCAAGCAGGCGATTTCGGAGCTCGTGGGCCAAGAGAACGTGAGAGAGGCACGTGGCATCCCAGTCA
AATTAATCAAAAGCAAGAAAATGGCTGGGAGAGCTGTCTTGTTGGCAGGGCCTACTGAAACTGGAAAGACAGCCTTGGCT
CTGGCTATTGCTCAGGAACTGGGCAGTAAAATTCCTTTCTGCACGATGGTGGCTAGCGAATATACTCAACGGAGATGGAG
AAGACAGAGGTTCTGATGGAGAACTTGCTCAGGGGTATTGGGCTGTGGATAAAGGAGACTAAGGAAGTTTATGAAAGGGA
GGTGACAGAGCTCACTCCCTGTGAGACAAAGAGTCCTATGGATGGGTATGGCAAAACCATCAGCCATGTAATCATAGGGC
TGAAGACTGCCAAAGGAACCAAACAGAGGAAGCTGGATCCCAGTATTTTTTGAAAGTTTGCAGAAAGAATGAGTAAAGTC
TGGAGATGCGATTTACATTGAAGCTAACAGTGGAGCTGTGAAGAGGCAAGATAGGTGTAACACCTATGCTACAGAATTTG
ACCTTGAGGCTGAAGAGTACGTCCCTTTGCCAAAGGGAGATGTGCACAAGAAGAAGGAAATCATACAAGATGTGACTTTG
CTTGAACTGGACGTGGCTGATTCACGGCCTCAGGGTGGGCAAGATATTTTGTCTATGACGAGCCAGTTGTTGGAGCCAAA
AAAGACAGAGATCACAGATAAACTTCGAGGGGAGATCAACAAGGTGGTGAACAAATGCACTGACCAGGGCATTGCAGAGT
TGGTCCCTGGAGTGGTT

Alignment

ORF - retro_rnor_424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.06 %
• Parental protein coverage: 65.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAG
          MKIEEVKSTT..Q.IASHSH.KGLGLD...LAKQA.S.LVGQEN.REA.G..V.LIKSKKMAGRAVLLAG
Retrocopy MKIEEVKSTTMMQHIASHSHMKGLGLDDRRLAKQAISELVGQENVREARGIPVKLIKSKKMAGRAVLLAG

Parental  PPGTGKTALALAIAQELGSKVPFCPMVGSE-VYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELT
          P..TGKTALALAIAQELGSK.PFC.MV.SE..YSTE..KTEVLMEN..R.IGL.IKETKEVYE.EVTELT
Retrocopy PTETGKTALALAIAQELGSKIPFCTMVASE<IYSTEMEKTEVLMENLLRGIGLWIKETKEVYEREVTELT

Parental  PCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSI-FESLQKERVEAGDVIYIEANSGAVKRQGRCDT
          PCET..PM.GYGKTISHVIIGLKTAKGTKQ.KLDPSI.FESLQKE.V..GD.IYIEANSGAVKRQ.RC.T
Retrocopy PCETKSPMDGYGKTISHVIIGLKTAKGTKQRKLDPSI>FESLQKE*VKSGDAIYIEANSGAVKRQDRCNT

Parental  YATEFDLEAEEYVPLPKGDVHKKKEIIQDVTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGE
          YATEFDLEAEEYVPLPKGDVHKKKEIIQDVTL..LDVA..RPQGGQDILSM..QL..PKKTEITDKLRGE
Retrocopy YATEFDLEAEEYVPLPKGDVHKKKEIIQDVTLLELDVADSRPQGGQDILSMTSQLLEPKKTEITDKLRGE

Parental  INKVVNKYIDQGVAELVPGVL
          INKVVNK..DQG.AELVPGV.
Retrocopy INKVVNKCTDQGIAELVPGVV

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	14.67 RPM
SRP017611_kidney	0.00 RPM	13.96 RPM
SRP017611_liver	0.00 RPM	9.95 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_424 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_424 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_424 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
Myotis lucifugus	ENSMLUG00000004254	1 retrocopy	retro_mluc_1421,
Mus musculus	ENSMUSG00000030079	1 retrocopy	retro_mmus_493,
Ochotona princeps	ENSOPRG00000011261	1 retrocopy	retro_opri_1115,
Rattus norvegicus	ENSRNOG00000013195	2 retrocopies	retro_rnor_2883, retro_rnor_424 ,