RetrogeneDB ID: retro_rnor_156

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:143708536..143709355(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000043487
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RGD1309748
• Ensembl ID: ENSRNOG00000002545
• Aliases: None
• Description: None

Sequence

>retro_rnor_156
ATGGAGGAGCAACAGAAGGACCGTGAGGCCGAGGTCGCAGGGCCCTGGTTTTCCAAGTGGGAGCGTCAGTGCCTGGCCGA
GGCGGAGCAGCTGTCCCCCGAGCTGCAGGAGGAGGCGGCTGCTGATGCGGCGGGGCTCAAGATCGAGCGCCAGAGGCTCT
GGCACCTATTCCAGATCTCAGCCACCGCTGTGGCCCAGCTCTACAAAGATTCCGGGTGCCAGCAGCCAGGACTCTCTATG
TGGGACCCCTTTCAGAACGCGGCCATGGCTGTGACCAGCCTTTACAAAGAAAGCGGGGATGCCTCCCAGCGAAGTTTTGA
ACTGGGCGTCCAGGTTGGCTACCAGCGTCGTGTGAGAGATGTTCTGGAATGGGTGAAGAAGGGTAGGAGCATCATTCGCC
GGGAAGACCTCATAAGCTTCCTCTGTGGCAAAGTTCCCCCCACACCCCCGCCGCTCCGCACCTCCTGGACGTCCCCCAGG
CCACCCGCGGCTGCCTCCACTCAAGCTGCTGCCACTGAGTCTAGCGCACCTGTGGATGTCGACCTGCAGCCCTTCCACGA
GGCCATTGCGCTTCATGGCCTCAGTGGTGCCATGGCAAGCATCAGCATGCGATCTGGCACTCCAAGTTCATCACAAGATG
GAGGTATTGCCAGCAGTGGGCGTCGGAAAAGTAGCTTCCTTGAAGATGATCAGAACCCCTTGAGCTCAGAAGAACTGGCT
CTCCGCCTGGACAGTGGGGGAATCCGCAAGCGCACATCTGCCCAGCTTGGTGATGGCGCTACAGACTCTCCATCACACAA
GCGCAACCGAATGGTCTAA

Alignment

ORF - retro_rnor_156 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEERKEEGEAEIQEHGPEHWFSKWERQCLAEAEQDEQLSPELQEEAAA-AAQPEHKQQKLWHLFQNSATA
          MEE.....EAE....GP..WFSKWERQCLAEA...EQLSPELQEEAAA.AA......Q.LWHLFQ.SATA
Retrocopy MEEQQKDREAEVA--GP--WFSKWERQCLAEA---EQLSPELQEEAAADAAGLKIERQRLWHLFQISATA

Parental  VAQLYKDRVCQQPGLSLWVPFQNAATAVTNLYKESVDTHQRSFDIGIQIGYQRRNKDVLAWVKKRRRTIR
          VAQLYKD..CQQPGLS.W.PFQNAA.AVT.LYKES.D..QRSF..G.Q.GYQRR..DVL.WVKK.R..IR
Retrocopy VAQLYKDSGCQQPGLSMWDPFQNAAMAVTSLYKESGDASQRSFELGVQVGYQRRVRDVLEWVKKGRSIIR

Parental  REDLISFLCGKVPPP----RNSRAPPRLTVVSPNRATSTETSSSVETDLQPFREAIALHGLSGAMASISV
          REDLISFLCGKVPP.....R.S...PR........A..TE.S..V..DLQPF.EAIALHGLSGAMASIS.
Retrocopy REDLISFLCGKVPPTPPPLRTSWTSPRPPAAASTQAAATESSAPVDVDLQPFHEAIALHGLSGAMASISM

Parental  RSSTPGSPTHVSSGPNASRRRNGLHDVDLNTFITEEMALHLDNGGTRKRTSAQCGDVITDSPTHKRNRML
          RS.TP.S...........R....L.D.D.N....EE.AL.LD.GG.RKRTSAQ.GD..TDSP.HKRNRM.
Retrocopy RSGTPSSSQDGGIASSGRRKSSFLED-DQNPLSSEELALRLDSGGIRKRTSAQLGDGATDSPSHKRNRMV

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	2.08 RPM	53.85 RPM
SRP017611_kidney	0.21 RPM	41.03 RPM
SRP017611_liver	0.00 RPM	20.78 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_156 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_156 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_156 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4765
Pan troglodytes	retro_ptro_3172
Gorilla gorilla	retro_ggor_2968
Pongo abelii	retro_pabe_163
Mus musculus	retro_mmus_3460
Sus scrofa	retro_sscr_1177
Canis familiaris	retro_cfam_147
Equus caballus	retro_ecab_1091

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010719	2 retrocopies	retro_amel_1715, retro_amel_88,
Canis familiaris	ENSCAFG00000018981	1 retrocopy	retro_cfam_147,
Cavia porcellus	ENSCPOG00000010925	1 retrocopy	retro_cpor_101,
Dasypus novemcinctus	ENSDNOG00000015893	3 retrocopies	retro_dnov_1575, retro_dnov_2266, retro_dnov_827,
Equus caballus	ENSECAG00000009430	1 retrocopy	retro_ecab_1091,
Homo sapiens	ENSG00000182831	1 retrocopy	retro_hsap_4765,
Gorilla gorilla	ENSGGOG00000010744	1 retrocopy	retro_ggor_2968,
Monodelphis domestica	ENSMODG00000005378	2 retrocopies	retro_mdom_1716, retro_mdom_299,
Mustela putorius furo	ENSMPUG00000014707	1 retrocopy	retro_mputfur_44,
Mus musculus	ENSMUSG00000022507	1 retrocopy	retro_mmus_3460,
Nomascus leucogenys	ENSNLEG00000010106	1 retrocopy	retro_nleu_2348,
Otolemur garnettii	ENSOGAG00000003909	1 retrocopy	retro_ogar_74,
Pongo abelii	ENSPPYG00000007088	1 retrocopy	retro_pabe_163,
Pan troglodytes	ENSPTRG00000007751	1 retrocopy	retro_ptro_3172,
Rattus norvegicus	ENSRNOG00000002545	2 retrocopies	retro_rnor_156 , retro_rnor_1928,
Sus scrofa	ENSSSCG00000028454	1 retrocopy	retro_sscr_1177,
Ictidomys tridecemlineatus	ENSSTOG00000009324	1 retrocopy	retro_itri_137,