RetrogeneDB ID: retro_rnor_61

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:66867606..66868281(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000034071
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSRNOG00000046585
• Aliases: None
• Description: None

Sequence

>retro_rnor_61
ATGTCGGTGTTCGGGAAGCTGTTCGGGGCTGGATGGGGTAAGGCGGGCAAGGGCGACCCGACCCCCCAGGAGGCCATACA
GCGACTTCGGGACACGGAGGAAATGCTAAGCAAGAAACAAGAGTTTCTGGAGAAGAAGATCGAGCAGGAGCTGACGGCTG
CCAAGAAGCACGGCACCAAAAATAAGCGCGCGGCCTTGCAGGCTCTGAAGCGCAAGAAGAGGTATGAGAAGCAGCTGGCA
CAGATTGATGGCACCCTGTCAACCATCGAGTTCCAGCGGGAGGCCCTAGAGAATGCCAACACCAACACGGAGGTGCTCAA
GAACATGGGCTATGCCGCCAAGGCCATGAAGGCTGCCCACGACAACATGGACATTGATAAAGTGGATGAGTTAATGCAGG
ACATTGCTGACCAGCAAGAACTTGCAGAACAGACTTCCACAGCTATCTCCAAACCTGTGGGCTTTGGAGAAGAGTTTGAC
AAGGATGAGCTCATGGCAGAGCTGGAGGAACTCGAACAAGAGGAGCTAGACAAGAATTTGTTGGAGATCAGTGGGCCCGA
AACAGTCCCTCTACCAAATGTCCCCTCTGTAGCCCTACCATCCAAACCCGCCAAGAAGAAGGAGGAGGAAGACGACGACA
TGAAGGAGTTGGAGAACTGGGCGGGATCCATGTAA

Alignment

ORF - retro_rnor_61 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVFGKLFGAGGGKAGKGGPTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKETTAALQALK
          MSVFGKLFGAG.GKAGKG.PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTK...AALQALK
Retrocopy MSVFGKLFGAGWGKAGKGDPTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRAALQALK

Parental  RKKRYEKQLAQIDGTLSTIEFQREALENANTNTEVLKNMGYAAKAMKAAHDNMDIDKVDELMQDIADQQE
          RKKRYEKQLAQIDGTLSTIEFQREALENANTNTEVLKNMGYAAKAMKAAHDNMDIDKVDELMQDIADQQE
Retrocopy RKKRYEKQLAQIDGTLSTIEFQREALENANTNTEVLKNMGYAAKAMKAAHDNMDIDKVDELMQDIADQQE

Parental  LAEEISTAISKPVGFGEEFDEDELMAELEELEQEELDKNLLEISGPETVPLPNVPSVALPSKP
          LAE..STAISKPVGFGEEFD.DELMAELEELEQEELDKNLLEISGPETVPLPNVPSVALPSKP
Retrocopy LAEQTSTAISKPVGFGEEFDKDELMAELEELEQEELDKNLLEISGPETVPLPNVPSVALPSKP

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	47.45 RPM	20.27 RPM
SRP017611_kidney	29.24 RPM	14.24 RPM
SRP017611_liver	12.91 RPM	6.59 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_61 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_61 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_61 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009038	1 retrocopy	retro_amel_1612,
Bos taurus	ENSBTAG00000013387	1 retrocopy	retro_btau_1103,
Canis familiaris	ENSCAFG00000007478	1 retrocopy	retro_cfam_1304,
Choloepus hoffmanni	ENSCHOG00000007288	1 retrocopy	retro_chof_2518,
Equus caballus	ENSECAG00000008311	1 retrocopy	retro_ecab_496,
Felis catus	ENSFCAG00000025893	1 retrocopy	retro_fcat_1835,
Homo sapiens	ENSG00000101421	1 retrocopy	retro_hsap_1339,
Gorilla gorilla	ENSGGOG00000007775	1 retrocopy	retro_ggor_29,
Macaca mulatta	ENSMMUG00000008084	1 retrocopy	retro_mmul_2178,
Mustela putorius furo	ENSMPUG00000017821	2 retrocopies	retro_mputfur_1302, retro_mputfur_697,
Nomascus leucogenys	ENSNLEG00000010020	1 retrocopy	retro_nleu_1822,
Pongo abelii	ENSPPYG00000010931	1 retrocopy	retro_pabe_1111,
Pan troglodytes	ENSPTRG00000013408	1 retrocopy	retro_ptro_915,
Pteropus vampyrus	ENSPVAG00000010293	1 retrocopy	retro_pvam_973,
Rattus norvegicus	ENSRNOG00000046585	1 retrocopy	retro_rnor_61 ,
Tarsius syrichta	ENSTSYG00000013212	1 retrocopy	retro_tsyr_1453,