RetrogeneDB ID: retro_rnor_1406

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:65276188..65276956(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000038592
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rnf149
• Ensembl ID: ENSRNOG00000013946
• Aliases: None
• Description: Protein Rnf149 [Source:UniProtKB/TrEMBL;Acc:D3ZI66]

Sequence

>retro_rnor_1406
CACTCGAGTGGTACTCGGCCACGGTGAGCATCGAGAACAGGCAACATAGTCGTCATCATGATTAGCTACCCAAAAGGACG
GGAGATTTCTGATCTGGTGCAAAAAGGAATTCCAGTAAAAATGAGCATAGAGATTGGTACTCATCACATACAGGAGTTCA
TCAGCAGTCAGTCTGTGGTGTTTGCGGCCATTGCCTTCATCACGATGATGATTATCTCATTAGCATGGCTAATATTCTAT
TATAGACAGCGTTTCCTATATACTGGCTCACAGTTTGGAAGTCAGAATCATAGAAAGGAAACTAAGAAGGTTATTGGCCA
GCTTCCACTACGCACTGTAAAGCGTGGAGAGAAGGGAATCGATGTTGATGCTGAGAATTGTGCAGTGTGTATTGAAAACT
TTAAAGTCAAAGGTGTTATCAGAATCCTGCCATGCAAGCAGATTTTTCATAGAATATGCATTGACCCATGGCTTTTGGAT
CACCGAACGTGTCCAATGTGTAAACTTGATGTCATCAAAGCCCTCGGATATTGGGGGAACCCTGAGGATGCACAGGAGCT
AAGCATCCCAGAAGCTGCCCCAGGAAGTGTTTCTGTTGGGAATCTGAGTGTGAGAGTCCAAGATGAGGACAGGAGTGAAA
GCAACCTTCCACCATCTTCGTCAAGCGAGTTTGGGCCACACTGCCCTTGTCTTAAAGAAGATGCAGAGGAGGACACAACA
TTGCTAGGAGCCGGCAAGAGTGACCCTCAGCATGGAGGATCCATCTGT

Alignment

ORF - retro_rnor_1406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.28 %
• Parental protein coverage: 64.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YGNATEPMSHAGTGSIVVIMISYPKGREISDLVQKGIPVKMRIEIGTRHMQEFISGQSVVFVAIAFITMM
          ....T.P.....TG.IVVIMISYPKGREISDLVQKGIPVKM.IEIGT.H.QEFIS.QSVVF.AIAFITMM
Retrocopy HSSGTRPR*ASRTGNIVVIMISYPKGREISDLVQKGIPVKMSIEIGTHHIQEFISSQSVVFAAIAFITMM

Parental  IISLAWLIFYYIQRFLYTGSQFGSQNHRKETKKVIGQLPLHTVKHGEKGIDVDAENCAVCIENFKVKDVI
          IISLAWLIFYY.QRFLYTGSQFGSQNHRKETKKVIGQLPL.TVK.GEKGIDVDAENCAVCIENFKVK.VI
Retrocopy IISLAWLIFYYRQRFLYTGSQFGSQNHRKETKKVIGQLPLRTVKRGEKGIDVDAENCAVCIENFKVKGVI

Parental  RILPCKHIFHRICIDPWLLDHRTCPMCKLDVIKALGYWGDPEDAQDLPIPEAAPGSVSVGNLSVTVQDEE
          RILPCK.IFHRICIDPWLLDHRTCPMCKLDVIKALGYWG.PEDAQ.L.IPEAAPGSVSVGNLSV.VQDE.
Retrocopy RILPCKQIFHRICIDPWLLDHRTCPMCKLDVIKALGYWGNPEDAQELSIPEAAPGSVSVGNLSVRVQDED

Parental  RSESNLPSSSSSEFGPHRPCLKEDAEEDTALLGAGRSDPQHGGSIC
          RSESNLP.SSSSEFGPH.PCLKEDAEEDT.LLGAG.SDPQHGGSIC
Retrocopy RSESNLPPSSSSEFGPHCPCLKEDAEEDTTLLGAGKSDPQHGGSIC

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	0.07 RPM	29.48 RPM
SRP017611_kidney	0.00 RPM	54.50 RPM
SRP017611_liver	0.00 RPM	64.88 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1406 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1406 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012057	2 retrocopies	retro_chof_290, retro_chof_555,
Dasypus novemcinctus	ENSDNOG00000011956	3 retrocopies	retro_dnov_2168, retro_dnov_534, retro_dnov_580,
Macropus eugenii	ENSMEUG00000014821	1 retrocopy	retro_meug_417,
Myotis lucifugus	ENSMLUG00000007110	1 retrocopy	retro_mluc_1684,
Rattus norvegicus	ENSRNOG00000013946	2 retrocopies	retro_rnor_1406 , retro_rnor_2527,
Tursiops truncatus	ENSTTRG00000016450	1 retrocopy	retro_ttru_351,