RetrogeneDB ID: retro_rnor_1776

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:10794344..10794691(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000047465
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ensa
• Ensembl ID: ENSRNOG00000048617
• Aliases: None
• Description: Alpha-endosulfine [Source:UniProtKB/Swiss-Prot;Acc:P60841]

Sequence

>retro_rnor_1776
TCCCAGAAACAAGAAGAAGAAAACCCTGCGGAGGAAACCGGCGAGGAGAAGCAGGATACACAGGAGAAAGAAGGTATTCT
TCCTGAGAAGGCTGAGGAGGCAAAGCTAAGGCCAAATATCCAAGCTTAGGACAAAAGCCTGGAAGCTCCGACTTCCTCAT
GAAGAGATGCCAGAAAGGGCAAACGTACTTTGACTCAGGAGAGTACAACGTGGCCAAAACCAAGATAAAGAACAAGCAGC
TACCGAGTGCAGGAGCAGACAAGAACCTGGTGACCGGTGACCACATCCCCACCCTACAGGACCTGCCCCAGAGAAAGTCC
TCGCTCGTCACCAGCAAGCTTGCGGGG

Alignment

ORF - retro_rnor_1776 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 95.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SQKQEEENPAEETGEEKQDTQEKEGILPEKAEEAKL-KAKYPSLGQKPGGSDFLMKRLQKGQKYFDSGDY
          SQKQEEENPAEETGEEKQDTQEKEGILPEKAEEAKL.KAKYPSLGQKPG.SDFLMKR.QKGQ.YFDSG.Y
Retrocopy SQKQEEENPAEETGEEKQDTQEKEGILPEKAEEAKL<KAKYPSLGQKPGSSDFLMKRCQKGQTYFDSGEY

Parental  NMAKAKMKNKQLPSAGADKNLVTGDHIPTPQDLPQRKSSLVTSKLAG
          N.AK.K.KNKQLPSAGADKNLVTGDHIPT.QDLPQRKSSLVTSKLAG
Retrocopy NVAKTKIKNKQLPSAGADKNLVTGDHIPTLQDLPQRKSSLVTSKLAG

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	0.07 RPM	148.97 RPM
SRP017611_kidney	0.35 RPM	23.80 RPM
SRP017611_liver	0.00 RPM	7.60 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1776 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1776 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1776 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000143420	3 retrocopies	retro_hsap_1449, retro_hsap_2208, retro_hsap_2452,
Mus musculus	ENSMUSG00000038619	1 retrocopy	retro_mmus_2675,
Oryctolagus cuniculus	ENSOCUG00000003267	3 retrocopies	retro_ocun_296, retro_ocun_396, retro_ocun_722,
Otolemur garnettii	ENSOGAG00000005863	3 retrocopies	retro_ogar_1769, retro_ogar_1911, retro_ogar_2262,
Pongo abelii	ENSPPYG00000000893	2 retrocopies	retro_pabe_1803, retro_pabe_2081,
Rattus norvegicus	ENSRNOG00000048617	1 retrocopy	retro_rnor_1776 ,