RetrogeneDB ID: retro_rnor_2040

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:24212091..24213303(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cd2ap
• Ensembl ID: ENSRNOG00000011987
• Aliases: Cd2ap, CMS
• Description: CD2-associated protein [Source:RefSeq peptide;Acc:NP_852140]

Sequence

>retro_rnor_2040
ATGGTTGACCGTATTGTTGAGTATGAATACCACGCTGTACGTGATGATGAGTTAACTATCTGAGCTGGGGAAATCATCCA
AAATGTGAAAAAACTACAGGAAGAAGGATGGCTAAAAGGATATCTAAAGGGGAGATCAGGGATGTTCCCTGACAAATTTG
TTAAGGAAATTAAAAGAAAGACAGAACCCAAGGATGACAATTTGCCCGTCAAATGGGAAAGGCATGGAAATATAGCAAGT
ATTGTATAGCAAATCAGCACTTAAGGACTTCCAGCTGGAGGAATCCAGCCACATCCACAAACCAAAGCTATTAAGAACAC
AAAAATGTGTCAGTGTAAAATTCTTTTTGACTACTCTCCACAAAATGAGGACGAACTGTAATTGACTGTGGAGGATGACA
TTGAAGAGGTAGAAGAAGGTTGGTGGAGTGGAATCCTGAACAGTAAGTTGGGACTGCTTCCCTCAAACTTTTTGAAAGAA
TTAAGAGGTCACAGATGACGGTAAAACTCAACAATGCTCAGGAGGAATCAGATGTTCTTTGAGTGGCCCTACTTCACCTA
TTCCTTCTCCAGGGAATGGATGTGAACCAGTTCCTGGATCAGCTACACAGCCAAAGAAGATCTGAGGAATTAGATTTGGA
GACATCTTTAAAAATGCTCTGTGAAACTTACAAGAAGAACTTCCTGTGGTGAAACAGAGGAGAAAAAAAAATCAGAAAAT
CCACTAATCCTACAGTCACTGGGCTCTAGAACCCAGAATATGGAGGTAACAAAAACAGACATTGATGGCAAGATTAGAGC
TAAGGAATATTGTAGAACTTTATTTCCCTGTGTAGGAAAAAATGAAGTGAACTTAAGTTTAGAGAAGGGGAGATTGATAA
TTCATTTGATAAGTAAGGTGACTGGAGAAGTGGGCTGGTGGAAAGGTGAACTGAATGGTAAAGAAGGAGTGTTTCCAGAT
AACTTTGCTGTTCAGATAAGTGAACTAGATAAAGACTTTCCAAAACTAAAGAAACCACCTCCTCCTGCAAAAGGTCCAGC
TCCAAAGCCGGACCTGTTAGCTGCAGAGAAGAAAACTTTTCCTCTAAAGGCTGAAGACAAAGATGAAAAATCACTGCTAG
AACAAAAATCTAAATCAGCAGTGGAAGTCTTACCCAAAAAGCTTACTCCATCTACCAAAGCCCCTAGTTTACTGAGGTCT
TCTGGAGCAATG

Alignment

ORF - retro_rnor_2040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.12 %
• Parental protein coverage: 64.05 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LVDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKEIKRETEPKDDNLPI
          .VD.IVEY.Y.AV.DDELTI..GEII.NVKKLQEEGWL.G.L.GR.GMFPD.FVKEIKR.TEPKDDNLP.
Retrocopy MVDRIVEYEYHAVRDDELTI*AGEIIQNVKKLQEEGWLKGYLKGRSGMFPDKFVKEIKRKTEPKDDNLPV

Parental  KRERPGNVASLVQRISTYGLPAGGIQPHPQTKAMKKKTKKRQCKVLFEYSPQNEDELELTVGDVIDVIEE
          K.ER.GN.AS.V..IST.GLPAGGIQPHPQTKA.K..TK..QCK.LF.YSPQNEDEL.LTV....D.IEE
Retrocopy KWERHGNIASIV*QIST*GLPAGGIQPHPQTKAIKN-TKMCQCKILFDYSPQNEDEL*LTVE---DDIEE

Parental  VEEGWWSGTLNNKLGLFPSNFVKEL-ESTDDGE-MHDAQEESEV-SLTGPTSPMPSPGNGSEPAPGSVTQ
          VEEGWWSG.LN.KLGL.PSNF.KEL.E.TDDG.....AQEES.V.SL.GPTSP.PSPGNG.EP.PGS.TQ
Retrocopy VEEGWWSGILNSKLGLLPSNFLKEL>EVTDDGK>LNNAQEESDV<SLSGPTSPIPSPGNGCEPVPGSATQ

Parental  PKKIRGVGFGDIFKEG-SVKLRTRTSSSETEEKK-SEKPLILQSLGSRTQNVEVTKPDIDGKIKAKEYCK
          PKKI.G..FGDIFK...SVKL..RTS..ETEE...SE.PLILQSLGSRTQN.EVTK.DIDGKI.AKEYC.
Retrocopy PKKI*GIRFGDIFKNA<SVKLTRRTSCGETEEXXXSENPLILQSLGSRTQNMEVTKTDIDGKIRAKEYCR

Parental  TVFPYTGTNEDELTFREGE-IIHLISKETGEAGWWKGELNGKEGVFPDNFAVQISELDKDFPKPKKPPPP
          T.FP..G.NE..L....G..IIHLISK.TGE.GWWKGELNGKEGVFPDNFAVQISELDKDFPK.KKPPPP
Retrocopy TLFPCVGKNEVNLSLEKGRLIIHLISKVTGEVGWWKGELNGKEGVFPDNFAVQISELDKDFPKLKKPPPP

Parental  AKGPAPKPDPLAGEKKTFPLKAEDRDEKSLLEQKPSKPAAPQVPPKKPTPPTKANNLLRSPGTM
          AKGPAPKPD.LA.EKKTFPLKAED.DEKSLLEQK.....A..V.PKK.TP.TKA..LLRS.G.M
Retrocopy AKGPAPKPDLLAAEKKTFPLKAEDKDEKSLLEQK--SKSAVEVLPKKLTPSTKAPSLLRSSGAM

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	15.17 RPM
SRP017611_kidney	0.00 RPM	100.35 RPM
SRP017611_liver	0.00 RPM	36.64 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2040 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2040 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000009776	1 retrocopy	retro_mluc_2422,
Mus musculus	ENSMUSG00000061665	1 retrocopy	retro_mmus_1604,
Oryctolagus cuniculus	ENSOCUG00000005026	1 retrocopy	retro_ocun_307,
Rattus norvegicus	ENSRNOG00000011987	1 retrocopy	retro_rnor_2040 ,