RetrogeneDB ID: retro_rnor_2278

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:28503988..28504317(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000040044
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Znhit1
• Ensembl ID: ENSRNOG00000001418
• Aliases: None
• Description: zinc finger, HIT domain containing 1 [Source:RefSeq peptide;Acc:NP_001258279]

Sequence

>retro_rnor_2278
CAGGCAGAGGCGGATCAACAGTTGGAGGTGTTAGAGAACAACTTCCAGGATGACCCCCACGCCGGCCTCCCCCAGCTGGG
CAAGAGACTACCTCAGTTCGATGATGATGCAGACACAGGAAAGAAAAAGAAGAAAACTCGAGGTGACCACTTCAAACTTC
GCTTACCCAAAAACTTCCAGGCTTTGCTGGAGGAGCAGAACCTGAATGCATCTGAGGGCCCCAACTACTTGACAGTCTGT
GTAGTTCCCCCATCTCGGCCCCAGCGTCCCTTCTGTGCTGGTGTGGCTTCCCATCCACGTATACCTGTGTAAGCTGTGGT
GCCCGGTAC

Alignment

ORF - retro_rnor_2278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 73.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QRRINRQLEALENDNFQDDPHAGLPQLGKRLPQFDDDADTGKKKKKTRGDHFKLRFRKNFQALLEEQNLS
          Q.....QLE.LEN.NFQDDPHAGLPQLGKRLPQFDDDADTGKKKKKTRGDHFKLR..KNFQALLEEQNL.
Retrocopy QAEADQQLEVLEN-NFQDDPHAGLPQLGKRLPQFDDDADTGKKKKKTRGDHFKLRLPKNFQALLEEQNLN

Parental  ASEGPNYLTACAGPPSRPQRPFCA-VCGFPSPYTCVSCGARY
          ASEGPNYLT.C..PPSRPQRPFCA..CGFPS.YTCVSCGARY
Retrocopy ASEGPNYLTVCVVPPSRPQRPFCA<WCGFPSTYTCVSCGARY

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	0.14 RPM	15.60 RPM
SRP017611_kidney	0.00 RPM	10.12 RPM
SRP017611_liver	0.07 RPM	4.71 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2278 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2278 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2278 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000010174	1 retrocopy	retro_etel_1701,
Homo sapiens	ENSG00000106400	1 retrocopy	retro_hsap_4012,
Gorilla gorilla	ENSGGOG00000016713	1 retrocopy	retro_ggor_2694,
Macaca mulatta	ENSMMUG00000006951	1 retrocopy	retro_mmul_2315,
Pan troglodytes	ENSPTRG00000019525	1 retrocopy	retro_ptro_2723,
Rattus norvegicus	ENSRNOG00000001418	2 retrocopies	retro_rnor_2162, retro_rnor_2278 ,