RetrogeneDB ID: retro_rnor_159

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:66147622..66148381(-)
• Located in intron of: ENSRNOG00000006001

Retrocopy information

• Ensembl ID: ENSRNOG00000027445
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Insig1
• Ensembl ID: ENSRNOG00000006859
• Aliases: None
• Description: Insulin-induced gene 1 protein [Source:UniProtKB/Swiss-Prot;Acc:Q08755]

Sequence

>retro_rnor_159
ATGCCCAGGCTGCACGACCACGTCTGGAGCTACCCAAGCGCGGGCGCTGCGAGGCCGTACAGCCTCCCGCGAGGCATGAT
TGCGGCGGCCCTCTGTCCGCAGGGCCCCGGAGCCCCCGAGCCCGAGCCCGCGCCCCAGGGCCAGCGAGAGGGAACCGCAG
CCTTCAGCACACGACCCGGCAGCTGGCACCATGACCTGGTGCAGCGGAGCCTCGTGCTCTTCTCATTTGGCGTGGTCCTG
GCTCTGGTGCTCAACCTGCTGCAGATCCAGCGGAATGTCACGCTCTTCCCGGACGAGGTGATAGCCACCATCTTCTCCTC
CGCCTGGTGGGTGCCCCCGTGCTGTGGCACGGCAGCCGCTGTTGTCGGCTTATTGTATCCCTGTATTGACAGTCACCTGG
GAGAACCACACAAGTTCAAGAGAGAGTGGGCCAGTGTCATGCGATGTATCGGGGTGTTTGTTGGCATCAACCATGCCAGT
GCCAAATTAGATTTCGCCAATAATGTGCAGCTGTCCCTGACACTGGCAGCCCTGTCCTTGGGCTTGTGGTGGACGTTTGA
TCGATCCCTAAGTGGCCTTGGGCTCGGGATCACCATCGCCTTCCTAGCCACGCTGATCACTCAGTTTCTTGTTTATAATG
GCGTCTACCAGTACACGTCCCCGGATTTCCTCTATATCCGTTCTTGGCTCCTGTGTATATTTTTCTCAGGAGGTGTCACA
GTGGGAAACATAGGACGACAGTTAGCTCACAGTGACTGA

Alignment

ORF - retro_rnor_159 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.59 %
• Parental protein coverage: 96.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPRLHDHVWSYPSAGAARPYSLPRGMIAAALCPQGPGAPEPEPAPRGQREGTAGFSARPGSWHHDLVQRS
          MPRLHDHVWSYPSAGAARPYSLPRGMIAAALCPQGPGAPEPEPAP.GQREGTA.FS.RPGSWHHDLVQRS
Retrocopy MPRLHDHVWSYPSAGAARPYSLPRGMIAAALCPQGPGAPEPEPAPQGQREGTAAFSTRPGSWHHDLVQRS

Parental  LVLFSFGVVLALVLNLLQIQRNVTLFPDEVIATIFSSAWWVPPCCGTAAAVVGLLYPCIDSHLGEPHKFK
          LVLFSFGVVLALVLNLLQIQRNVTLFPDEVIATIFSSAWWVPPCCGTAAAVVGLLYPCIDSHLGEPHKFK
Retrocopy LVLFSFGVVLALVLNLLQIQRNVTLFPDEVIATIFSSAWWVPPCCGTAAAVVGLLYPCIDSHLGEPHKFK

Parental  REWASVMRCIAVFVGINHASAKLDFANNVQLSLTLAALSLGLWWTFDRSRSGLGLGITIAFLATLITQFL
          REWASVMRCI.VFVGINHASAKLDFANNVQLSLTLAALSLGLWWTFDRS.SGLGLGITIAFLATLITQFL
Retrocopy REWASVMRCIGVFVGINHASAKLDFANNVQLSLTLAALSLGLWWTFDRSLSGLGLGITIAFLATLITQFL

Parental  VYNGVYQYTSPDFLYIRSWLPCIFFSGGVTVGNIGRQLA
          VYNGVYQYTSPDFLYIRSWL.CIFFSGGVTVGNIGRQLA
Retrocopy VYNGVYQYTSPDFLYIRSWLLCIFFSGGVTVGNIGRQLA

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	0.14 RPM	45.29 RPM
SRP017611_kidney	0.07 RPM	32.52 RPM
SRP017611_liver	0.13 RPM	129.16 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_159 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_159 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_159 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001982	1 retrocopy	retro_chof_1185,
Cavia porcellus	ENSCPOG00000014739	1 retrocopy	retro_cpor_1173,
Loxodonta africana	ENSLAFG00000028120	1 retrocopy	retro_lafr_1207,
Myotis lucifugus	ENSMLUG00000028113	1 retrocopy	retro_mluc_2270,
Rattus norvegicus	ENSRNOG00000006859	1 retrocopy	retro_rnor_159 ,