RetrogeneDB ID: retro_rnor_875

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 12:30438942..30439768(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Aebp2
• Ensembl ID: ENSRNOG00000008929
• Aliases: None
• Description: zinc finger protein AEBP2 [Source:RefSeq peptide;Acc:NP_001100096]

Sequence

>retro_rnor_875
ATAGGCAGTACAATTTCTAGTGGACATTCAACTCCAGCCATGATGAATGGACAAGGGAGAGCTACTGCTTCAGGCAAACA
CATAGCCTATAACTGTTGTTGGAGCCAATGCCAGGAGTGCTTCAACTTCAGCCCAGACCTGGCAGACCACATTCGCTCCA
TGTATGTAGATTGACAGAGTGGAGGGTTATTCACTTGCTTGTGAATGGTTTTAAGGTGTATAACACCTCATCAAACAGTC
AGAGTTGGTTACAGCCACACATGCTGACCCACAGTAGAGACAAATCTTTCAAGTGGGTAGTTGGTGGCTGCAATGTCAAC
TTTGCTTCTCAGGGAGGACTAGCTCACCATGTACCCACAAACTTCAGTCAGTAGAATTCTTCAAAAGTTTCTAGCCAGCC
AAAGGCCAAAGAAGAATTTCTGTCTAAAGCTGGAATGAGCAAGAGGAGGAAACTAAAGAACAAAAGATGGCGCTCATAAT
AACCACCAGCACGTGATTTTTTCATGGANTAAACGCTGGATGTCATAATATACCGAGCTGTATGCTTTAACCTCTCAGCT
CATATGGAAAATTTAGGGAAGGAAGAGAGTGTTGTTTTTCATTGTACTGTAATAACTAAGAGAAAGGAGGAATCTGGAAA
GATAAACATTTTGTTTCATTAGATTCCCGAAGATATTCTGCCAGATGTATGGGTGATTGAAATTGAATGATATCAGTTAA
AAACTAAGGCAGTTCTTTAGCAAAGCTACCCCAAAATACTGCCTTGCTGTTGAACCCAAACATTTAAACAACAATGCCAC
AGAAGAGTTTGAAGAGAACTCTGATA

Alignment

ORF - retro_rnor_875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.02 %
• Parental protein coverage: 89.29 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IDSTISSGRSTPAMMNGQGSTAASSKHIAYNCCWDQCQACFNSSPDLADHIRSIHVDGQRGGVFVCL-WK
          I.STISSG.STPAMMNGQG...AS.KHIAYNCCW.QCQ.CFN.SPDLADHIRS..VD.Q.GG.F.CL...
Retrocopy IGSTISSGHSTPAMMNGQGRATASGKHIAYNCCWSQCQECFNFSPDLADHIRSMYVD*QSGGLFTCL<VN

Parental  GCKVYNTPSTSQSWLQRHMLTHSGDKPFKCVVGGCNASFASQGGLARHVPTHFSQQNSSKVSSQPKAKEE
          G.KVYNT.S.SQSWLQ.HMLTHS.DK.FK.VVGGCN..FASQGGLA.HVPT.FSQ.NSSKVSSQPKAKEE
Retrocopy GFKVYNTSSNSQSWLQPHMLTHSRDKSFKWVVGGCNVNFASQGGLAHHVPTNFSQ*NSSKVSSQPKAKEE

Parental  SPSKAGMNKRRKLKNKRRRS-LPRPHDFFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRK
          ..SKAGM.KRRKLKNKR.RS..P...DFF...TLD.I..RA.CFNLSAH.E.LGK..SVVFH.TVI.KRK
Retrocopy FLSKAGMSKRRKLKNKRWRS**PPARDFFMX*TLDVIIYRAVCFNLSAHMENLGKEESVVFHCTVITKRK

Parental  EESGKIKLLLHWMPEDILPDVWVNESERHQLRTKVV-HLSKLPKDTALLLDPNIYRTMPQKRLKSSSI
          EESGKI..L.H..PEDILPDVWV.E.E..QL.TK.V..L.KLP..TALLL.PNI..TMPQK.LK...I
Retrocopy EESGKINILFH*IPEDILPDVWVIEIE*YQLKTKAV<SLAKLPQNTALLLNPNI*TTMPQKSLKRTLI

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	12.08 RPM
SRP017611_kidney	0.00 RPM	17.86 RPM
SRP017611_liver	0.00 RPM	12.57 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_875 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_875 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_875 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007440	1 retrocopy	retro_cpor_431,
Myotis lucifugus	ENSMLUG00000006293	1 retrocopy	retro_mluc_1637,
Oryctolagus cuniculus	ENSOCUG00000016677	2 retrocopies	retro_ocun_1207, retro_ocun_1672,
Rattus norvegicus	ENSRNOG00000008929	1 retrocopy	retro_rnor_875 ,