RetrogeneDB ID: retro_rnor_1928

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:152044787..152045346(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

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

Sequence

>retro_rnor_1928
GCGGAGATCCAGGAGCACGGGCTGAGCACGGGTTCTCCAAGTGGGAGCGGCAGTGCCTCGCAGAGGCCGAGCAGGATGAG
CCCTGTCCGGCGAGCTGCGGGAGGAGGCGGCGGCCGCCGAGCAGCCCAAGGACAAGCAACAGAAGCTGTGGCATCTCTTC
CAGAACTCGGCCATGGCAGTGACTCAGCTCTACAAAGACTGAATGTGTCAGCAGCCAGGACTTTCTCTTTGGGTCCCCTT
CTAAAACGCAGCCACCGCCATCACCAACCTCTATAAAGAAAGTGTAGATACCCATCAGCGAAGTTTTGATATTGGAATTC
AGATTGGCAATTAGCGACGCAATAATAAGGATGTGCTGGCCTGGGTTAAAAAGCGCAGAAGAACTATTCCTCGAGAAGAC
TTGATTAGCTTCCTATGTGGAAAGGTTCCTCCACCACAAAACTCTAGAGCTCCCCCAAGACTGACTGTAGTGTTCCCTAA
CAGGGCTACTTCAACGGAAGCTAGCTCATCTGTAGAGACTGATTTGCAACCCTTCCGGGAAGCCATAACTCTGCATGGT

Alignment

ORF - retro_rnor_1928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.77 %
• Parental protein coverage: 67.64 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AEIQEHG-PEHWFSKWERQCLAEAEQDEQ-LSPELQEEAAAAAQPEHKQQKLWHLFQNSATAVAQLYKDR
          AEIQEHG..EH.FSKWERQCLAEAEQDE..LS.EL.EEAAAA.QP..KQQKLWHLFQNSA.AV.QLYKD.
Retrocopy AEIQEHG<AEHGFSKWERQCLAEAEQDEP<LSGELREEAAAAEQPKDKQQKLWHLFQNSAMAVTQLYKD*

Parental  VCQQPGLSLWVPFQNAATAVTNLYKESVDTHQRSFDIGIQIGY-QRRNKDVLAWVKKRRRTIRREDLISF
          .CQQPGLSLWVPF.NAATA.TNLYKESVDTHQRSFDIGIQIG...R.NKDVLAWVKKRRRTI.REDLISF
Retrocopy MCQQPGLSLWVPF*NAATAITNLYKESVDTHQRSFDIGIQIGN*RRNNKDVLAWVKKRRRTIPREDLISF

Parental  LCGKVPPPRNSRAPPRLTVVSPNRATSTETSSSVETDLQPFREAIALHG
          LCGKVPPP.NSRAPPRLTVV.PNRATSTE.SSSVETDLQPFREAI.LHG
Retrocopy LCGKVPPPQNSRAPPRLTVVFPNRATSTEASSSVETDLQPFREAITLHG

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	0.22 RPM	53.85 RPM
SRP017611_kidney	0.00 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_1928 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1928 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1928 has 0 orthologous retrocopies within eutheria group .

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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,