RetrogeneDB ID: retro_rnor_255

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:248214032..248215196(-)
• Located in intron of: ENSRNOG00000036911

Retrocopy information

• Ensembl ID: ENSRNOG00000036910
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSRNOG00000023814
• Aliases: None
• Description: Protein Rimklb [Source:UniProtKB/TrEMBL;Acc:D3ZJ79]

Sequence

>retro_rnor_255
ATGTGTAGCTCTGTGACTGGTAAGCTGTGGTTCTTGACAGATCGTCGCATCCAAGAAGACTACCCACAGAAAGAGATCCT
AAGAGCTCTGAAGGCCAAATGCTGTGAAGAGGAATTGGACTTTAGGGCTGTAGTGATGGACGAGGTGGTGCTGACAGTCG
AGCAAGGAAATCTGGGTCTGCGGATCAATGGAGAGCTGATCTCTGCCTACCCACAGGTGGTGGTAGTGAGAGTTCCAACC
CCATGGGTGCAGAGCGACAGTGATATCACTGTTTTGCGCCACCTAGAGAAAATGGGGTGCCGGCTGATGAACCGGCCTCA
AGCCATCCTGAACTGTGTTGATAAATTCTGGACGTTTCAAGAGCTGGCTGGGCACGGTGTGCCTCTACCAGATACTTTTT
CTTACGGTGGCCACGAAAACTTTTCTAAAATGATTGATGAAGCGGAAGTGCTGGAGTTCCCAATGGTGGTGAAGAATACA
CGGGGTCATAGAGGCAAAGCTGTTTTCTTGGCACGAGATAAACACCATTTAGCTGATCTAAGCCATCTTATTCGGCACGA
AGCTCCATATTTGTTCCAGAAATATATCAAAGAGTCTCATGGAAGGGATGTGAGAGTCATTGTTGTGGGAGGCCGTGTAG
TTGGCACCATGCTACGCTGTTCGACAGATGGAAGGATGCAAAGCAACTGTTCCCTAGGTGGTGTGGGGATGATGTGCTCA
TTGAGTGAACAAGGGAAGCAGCTAGATATCCAGGTGTCTAATATCCTGGGGATGGATGTGTGTGGCATTGACCTGTTGAT
GAAAGATGACGGCTCCTTCTGTGTCTGCGAGGCCAATGCAAATGTAGGTTTCATCGCCTTTGATAAGGCTTGTAATCTAG
ATGTAGCTGGTATCATAGCAGACTATGCTGCCTCCCTTCTGCCCGCTGGGCGGCTCACCCGGCGCATGTCCCTGCTCTCT
GTGGTGTCCACTGCCAGTGAGACCAGTGAGCCGGAGCTCGGTCCCCCTGCCAGCGCTGCTGTCGACAACATGAGCGCCAG
TTCCAGCTCTGTTGATAGCGACCCTGAAAGCACCACCGAGCGAGAGCTGCTCACCAAGCTCCCAGGGGGGCTGTTCAACA
TGAACCAGCTGCTAGCCAATGAAATCAAACTCCTGGTGGAGTGA

Alignment

ORF - retro_rnor_255 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLRINGELISAYPQVVVVRVPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNCVNKFWTFQELAGHGVP
          GLRINGELISAYPQVVVVRVPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNCV.KFWTFQELAGHGVP
Retrocopy GLRINGELISAYPQVVVVRVPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNCVDKFWTFQELAGHGVP

Parental  LPDTFSYGGHENFSKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKYIKE
          LPDTFSYGGHENFSKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKYIKE
Retrocopy LPDTFSYGGHENFSKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKYIKE

Parental  SHGRDVRVIVVGGRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNILGMDVCGIDLLMK
          SHGRDVRVIVVGGRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQGKQL.IQVSNILGMDVCGIDLLMK
Retrocopy SHGRDVRVIVVGGRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQGKQLDIQVSNILGMDVCGIDLLMK

Parental  DDGSFCVCEANANVGFIAFDKACNLDVAGIIADYAASLLPAGRLTRRMSLLSVVSTASETSEPELGPPAS
          DDGSFCVCEANANVGFIAFDKACNLDVAGIIADYAASLLPAGRLTRRMSLLSVVSTASETSEPELGPPAS
Retrocopy DDGSFCVCEANANVGFIAFDKACNLDVAGIIADYAASLLPAGRLTRRMSLLSVVSTASETSEPELGPPAS

Parental  AAVDNMSASSSSVDSDPESTTERELLTKLPGGLFNMNQLLANEIKLLVE
          AAVDNMSASSSSVDSDPESTTERELLTKLPGGLFNMNQLLANEIKLLVE
Retrocopy AAVDNMSASSSSVDSDPESTTERELLTKLPGGLFNMNQLLANEIKLLVE

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	0.93 RPM	5.10 RPM
SRP017611_kidney	1.26 RPM	3.28 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_255 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_255 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_255 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000166532	1 retrocopy	retro_hsap_2506,
Gorilla gorilla	ENSGGOG00000000332	1 retrocopy	retro_ggor_31,
Nomascus leucogenys	ENSNLEG00000002201	2 retrocopies	retro_nleu_1422, retro_nleu_1437,
Oryctolagus cuniculus	ENSOCUG00000013997	1 retrocopy	retro_ocun_1777,
Otolemur garnettii	ENSOGAG00000011440	2 retrocopies	retro_ogar_1183, retro_ogar_2985,
Pongo abelii	ENSPPYG00000004244	1 retrocopy	retro_pabe_1844,
Pan troglodytes	ENSPTRG00000004643	1 retrocopy	retro_ptro_1457,
Rattus norvegicus	ENSRNOG00000023814	1 retrocopy	retro_rnor_255 ,
Tarsius syrichta	ENSTSYG00000003996	1 retrocopy	retro_tsyr_1977,
Tursiops truncatus	ENSTTRG00000000699	3 retrocopies	retro_ttru_1672, retro_ttru_366, retro_ttru_460,
Vicugna pacos	ENSVPAG00000003954	1 retrocopy	retro_vpac_256,