RetrogeneDB ID: retro_rnor_2689

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:57045259..57045833(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cyb5d1
• Ensembl ID: ENSRNOG00000045742
• Aliases: Cyb5d1, RGD1559567
• Description: cytochrome b5 domain containing 1 [Source:RefSeq peptide;Acc:NP_001178819]

Sequence

>retro_rnor_2689
AACAACCAGCCAGAAGACCTATGGTGTCTTACCTTGGATTTGTTTGCAATCTAACACTGCTTCTACAGGAATTCAAATTT
GACCTCCTGTTGAAACCCATCCTGGAGGTTGCAGGCCAGGACATTAGTCAGTGTTTTGATCCAAAGACTAAAGACATTCA
CAAGCACATAGATCCACTGACCGGTTGCATGAGATACTGCACTCGGCGGGGCTGCTTTGTGCATATCCCGCCTTCTGGTC
CCTGTTCAGACTGGGCCAATGATTTCAGAACACCCTGGTGGAAGGGGCTAAATTACCAGGTGGGAAGTCTGCCCAGACCC
AGAACATCCATATTATCAACTCTCTTACATCACAGGAGCACATACTATAGGTGGGGCCTCTGAAGTCAATGTGGGAAATC
CTACACTGCTATCTCCCCTATAATGTACATGCTGCCAGCCACACATGGAAATACAATGGGAAGAATTTGAACATGGATCA
AACCCTGGATGAAAATGGGATCCGTGATGAAGAAGAGGATTTGGAATGTGAGCTTGTCCTAGGATTGTTGCATGATGGGG
AAATGTAAGTCTAT

Alignment

ORF - retro_rnor_2689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.38 %
• Parental protein coverage: 84.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HNQPEDLW-VSYLGFVYNLTPLVQEFKGDLLLKPILEVAGQDISHWFDPKTKDIRKHIDPLTGCVRYRTP
          .NQPEDLW.VSYLGFV.NLT.L.QEFK.DLLLKPILEVAGQDIS..FDPKTKDI.KHIDPLTGC.RY.T.
Retrocopy NNQPEDLW<VSYLGFVCNLTLLLQEFKFDLLLKPILEVAGQDISQCFDPKTKDIHKHIDPLTGCMRYCTR

Parental  RGRFVHIPPPLPRSDWANDFGIPWWKGLNYQV-GRLSAQTRNIRIINTLTSQEHTLEVGALDSMWEILHR
          RG.FVHIPP..P.SDWANDF..PWWKGLNYQV.G..SAQT.NI.IIN.LTSQEH.L.VG.L.SMWEILH.
Retrocopy RGCFVHIPPSGPCSDWANDFRTPWWKGLNYQV<GK-SAQTQNIHIINSLTSQEHIL*VGPLKSMWEILHC

Parental  YLPYNAHAASYTWKYDGKNLNMDQTLEENGIRDEEEEFDFLNMDGTLHTPAILLY
          YLPYN.HAAS.TWKY.GKNLNMDQTL.ENGIRDEEE........G.LH......Y
Retrocopy YLPYNVHAASHTWKYNGKNLNMDQTLDENGIRDEEEDLECELVLGLLHDGEM*VY

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	0.00 RPM	14.74 RPM
SRP017611_kidney	0.00 RPM	19.96 RPM
SRP017611_liver	0.00 RPM	6.99 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2689 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2689 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2689 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000044795	1 retrocopy	retro_mmus_7,
Rattus norvegicus	ENSRNOG00000045742	1 retrocopy	retro_rnor_2689 ,
Tursiops truncatus	ENSTTRG00000010293	1 retrocopy	retro_ttru_1469,