RetrogeneDB ID: retro_rnor_216

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:44137336..44137963(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000003860
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Myl6b
• Ensembl ID: ENSRNOG00000028837
• Aliases: None
• Description: Protein RGD1560334; Similar to Myosin light chain 1 slow a (Predicted) [Source:UniProtKB/TrEMBL;Acc:D3ZHA7]

Sequence

>retro_rnor_216
GTGCCTCCCAAGAAGGATGCTCCTGTGAAGAAACCTGCAGGGCCCTCCATCTCTAAGCGTGCTGCCAAGTCTACAGCAGG
GACCCTTCTAGCCAAGACCAAGGCAGAGCCAGCTGCCCCCCAGACCCCTACGAAAACCCAGGAGCCCCCTGTTGATCTCT
CCAAAGTGGTGATCGAATTTAACAAAGACCAGCTGGAGGAGTTCAGAGAGGCCTTTGAGCTGTTTGACCGAGTGGGTGAT
GGCAAGCTCCTGTACAGCCAGTGTTGGGGGGACCTGATACGGACCCTGGGCCAGAACCCTACCAATGCTGAGGTGCTCAA
GGTCCTGGGGAACCCCAAGAACAATGAGCTGAAGTCCCGGCGTGTAGACTTTGAGACATTCCTGCTTATGCTGCAGGCAG
TGGCCAAGCACCGGGACCAAGACACATATGAGGACTACCTAGACAGGCTTCGTGTGTTTGACAAAGAGGGCAACGGTAAA
GTCATGGGAGCGGAGCTCAGACACGTTCTGACCACTCTCGGAGAGAAGATGACTGAGGAAGAGGTAGAGACTGTTTTGGC
AGGCCATGAGGACAGCAACGACTGCATCAACTATGAGGTCTTCCTGAAGCACATCCTAAGCCTCTGA

Alignment

ORF - retro_rnor_216 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPPKKDAPVKKPAGPSISKPAAKSTAGTPLAKTKAEPAAPQTPVKTQEPPVDLSKVVIEFNKDQLEEFRE
          .PPKKDAPVKKPAGPSISK.AAKSTAGT.LAKTKAEPAAPQTP.KTQEPPVDLSKVVIEFNKDQLEEFRE
Retrocopy VPPKKDAPVKKPAGPSISKRAAKSTAGTLLAKTKAEPAAPQTPTKTQEPPVDLSKVVIEFNKDQLEEFRE

Parental  AFELFDRVGDGKILYSQC-GDLMRALGQNPTNAEVLKVLGNPKSDELKSRRVDFETFLPMLQAVAKHRDQ
          AFELFDRVGDGK.LYSQC.GDL.R.LGQNPTNAEVLKVLGNPK..ELKSRRVDFETFL.MLQAVAKHRDQ
Retrocopy AFELFDRVGDGKLLYSQCWGDLIRTLGQNPTNAEVLKVLGNPKNNELKSRRVDFETFLLMLQAVAKHRDQ

Parental  GTYEDYLEGLRVFDKEGNGKVMGAELRHVLTTLGEKMTEEEVETVLAGHEDSNGCINYEAFLKHILSL
          .TYEDYL..LRVFDKEGNGKVMGAELRHVLTTLGEKMTEEEVETVLAGHEDSN.CINYE.FLKHILSL
Retrocopy DTYEDYLDRLRVFDKEGNGKVMGAELRHVLTTLGEKMTEEEVETVLAGHEDSNDCINYEVFLKHILSL

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	22.50 RPM
SRP017611_kidney	0.00 RPM	9.70 RPM
SRP017611_liver	0.00 RPM	2.02 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_216 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_216 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000110	1 retrocopy	retro_cfam_1894,
Callithrix jacchus	ENSCJAG00000011620	3 retrocopies	retro_cjac_113, retro_cjac_2566, retro_cjac_2848,
Dasypus novemcinctus	ENSDNOG00000007592	1 retrocopy	retro_dnov_2073,
Homo sapiens	ENSG00000196465	1 retrocopy	retro_hsap_2383,
Gorilla gorilla	ENSGGOG00000003277	2 retrocopies	retro_ggor_1808, retro_ggor_2233,
Loxodonta africana	ENSLAFG00000012658	1 retrocopy	retro_lafr_734,
Macaca mulatta	ENSMMUG00000005214	1 retrocopy	retro_mmul_962,
Nomascus leucogenys	ENSNLEG00000026948	1 retrocopy	retro_nleu_369,
Oryctolagus cuniculus	ENSOCUG00000017368	1 retrocopy	retro_ocun_374,
Otolemur garnettii	ENSOGAG00000001521	3 retrocopies	retro_ogar_1918, retro_ogar_3179, retro_ogar_680,
Procavia capensis	ENSPCAG00000005927	2 retrocopies	retro_pcap_223, retro_pcap_242,
Pongo abelii	ENSPPYG00000004646	1 retrocopy	retro_pabe_2150,
Pan troglodytes	ENSPTRG00000023043	2 retrocopies	retro_ptro_1741, retro_ptro_2579,
Rattus norvegicus	ENSRNOG00000028837	2 retrocopies	retro_rnor_1432, retro_rnor_216 ,