RetrogeneDB ID: retro_rnor_2883

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:2648163..2649303(-)
• 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_2883
ATGAAGATTGAGGAGGTGAAGAGCACCACGAAGACGCAACGCATTGCCTCCCACAGCCACGTGAAGGGGCTGGGGCTGGA
TGAGAGCGGCCTGGCCAAGCAGGCGGCTTCGGGGCTCATAGGCCAGGAGAACGCGAGAGAGGCATGTGGCGTCATAGTCG
AATTAATCAAAAGCAAGAAAATGGCTGGAAGAGCTGTCTTGTTGGCAGGGCCTCCTGAAACTGGCAAGACAGCCTTGGCC
CTGGCTATTGCTCAGGAACTGGGCAGTAAAGTCCCTTTCTGCCCGATGGTGGGTAGTGAAGTATACTCAACTGAGATCAA
GAAGACAGAGGTGCTGATGGAGAACTTCCGAAGGGCTATTGGGCTGCGGATAAAGGAGACTAAGGAGGTTTATGAAGGGG
AGGTGACAGAGCTCACTCCCTGTGAGACAGAGAACCCCATGGGTGGGTATGGCAAAACTATCAGTCATGTAATCATAGGG
CTCAAGACTGCCAAAGGAACCAAACAGCTGAAGCTGGACCCCAGTATTTTTGAAAGTTTGCAGAAAGAACGAGTAGAGGC
TGGAGATGTGATTTACATTGAAGCAAACAGTGGAGCTGTGAAGAGGCAAGGCAGGTGTGACACCTATGCCACAGAGTTTG
ACCTTGAGGCTGAAAAGTACGTCCCTTTGCCAAACGGAGATGTGCACAAGAAGAAGGAAATCATACAGGATGTGACCTTG
CAATACTTGGACGTGGCCAATGTGCGGCCTCAGGGTGGGCAAGATATTCTGTCTATGATGGGCCAGTTGATGAAGCCAAA
AAAGACAGAGATCACAGATAAACTTCGAGGGGAGATCAACAAGGTGGTGAACAAATACATTGACCAGGGCGTTGCAGAGC
TGGTCCCTGGAGTGCTCTTTGTTGACGAGGTCCACATGCTGGATATCGAGTGCTTTACCTACCTGCACTGAGCCCTGGAG
TCCTCCATCACCCCCATTGTCATCTTTGCATCCAACGGAGCCAACTGTGTCATCAGGGGCACCGAGAACATCACTTCTCC
ACACGGCATCCCGTTAGACCTGCTGGACCGGGTGATAATCATCAGGACCATGCTGTATACGCCACAGGAGATGAAGCAGA
TCATTAAGATCCGAGCCCAG

Alignment

ORF - retro_rnor_2883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.58 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAG
          MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGL.GQENAREACGVIVELIKSKKMAGRAVLLAG
Retrocopy MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLIGQENAREACGVIVELIKSKKMAGRAVLLAG

Parental  PPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTP
          PP.TGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTP
Retrocopy PPETGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTP

Parental  CETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYA
          CETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYA
Retrocopy CETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYA

Parental  TEFDLEAEEYVPLPKGDVHKKKEIIQDVTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEIN
          TEFDLEAE.YVPLP.GDVHKKKEIIQDVTL..LDVAN.RPQGGQDILSMMGQLMKPKKTEITDKLRGEIN
Retrocopy TEFDLEAEKYVPLPNGDVHKKKEIIQDVTLQYLDVANVRPQGGQDILSMMGQLMKPKKTEITDKLRGEIN

Parental  KVVNKYIDQGVAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGI
          KVVNKYIDQGVAELVPGVLFVDEVHMLDIECFTYLH.ALESSI.PIVIFASN..NCVIRGTE.ITSPHGI
Retrocopy KVVNKYIDQGVAELVPGVLFVDEVHMLDIECFTYLH*ALESSITPIVIFASNGANCVIRGTENITSPHGI

Parental  PLDLLDRVMIIRTMLYTPQEMKQIIKIRAQ
          PLDLLDRV.IIRTMLYTPQEMKQIIKIRAQ
Retrocopy PLDLLDRVIIIRTMLYTPQEMKQIIKIRAQ

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	0.47 RPM	9.95 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2883 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2883 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,