RetrogeneDB ID: retro_rnor_2156

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:88317693..88318512(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tra2b
• Ensembl ID: ENSRNOG00000001783
• Aliases: Tra2b, Sfrs10, Srsf10
• Description: Transformer-2 protein homolog beta [Source:UniProtKB/Swiss-Prot;Acc:P62997]

Sequence

>retro_rnor_2156
AGAATTGCTCGTTCTTCTTCCCGAAGTGGAAGTGCTCATGGATCAGGGAAATCTGCACAGCATATACCTGTAAGGTCTCT
GTTCAAGGAAAATTAAGGCGTTCTAGGTTAAAGTCAAGATCCAGATCTGAATCTAGATCCAGATCCAGGAGAAGATCTAG
AAGGCATTATACAAAATCATGATCACGATCTGGCTCTCGTAGACAATGCAGGAGCAGGCCTTACAGCTGAGATTATCACA
AACACCACAGCAGTAACCATTCTCCCACGTCTACTCGAAGGCATCATGTGGGAACCAGGAAATCCTGACCCCCAACTATT
GTCTTGGAGTGTTTGGATTGAGCTTGTACACCACAGAAAGACATCTACGACAACTGTTCTCTAAATATTTTCCCATTGCT
GATGTGTTTATTGCGTATGACCAGCAATCTAAATGGTCAAGAGGATTTGTCTTTGTATATTTTGAAAATATAGATGATGC
AAGGAAACTAAAGAACGTGCCAATGGATTGGAGCTTGATGGACATTGAATTGGAGTCGATTTCTCTATAACTAAAAGGCC
ACATACCCCAACACCAGGAACTTATATGGGAAGACCAACTTGTGGCAGTTCACGATGCTTGGACTATTATGACAGAGGAT
ATGATCAGAGTTATGATGACCGGGACTATTATAACATAGGAGGTAGTGAAGGAGGAGGTGGATGGAGAGCAGCTCAAGAC
AGGGATCTAATTGGCAGAAGGCAGTCAACTTCTCCTTACTACAGTGGTGGATGGTACAGGTCTCCTTCTTGATCATGAGC
CTATACATCTTGTCACTAT

Alignment

ORF - retro_rnor_2156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.14 %
• Parental protein coverage: 96.18 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RESRSASRSGSAHGSGKSARHTPARSRSKED-SRRSRSKSRSRSESRSRSRRSSRRHYTRSRSRSRSHRR
          R..RS.SRSGSAHGSGKSA.H.P.RS..KE...RRSR.KSRSRSESRSRSRR.SRRHYT.S.SRS.S.R.
Retrocopy RIARSSSRSGSAHGSGKSAQHIPVRSLFKEN<LRRSRLKSRSRSESRSRSRRRSRRHYTKS*SRSGSRRQ

Parental  SRSRSYSRDYRRRHSHSHSPMSTRRRHVG-NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSI
          .RSR.YS.DY...HS..HSP.STRR.HVG.N.....PN.CLGVFGLSLYTTER.LR..FSKY.PIADV.I
Retrocopy CRSRPYS*DYHKHHSSNHSPTSTRRHHVG<NQEILTPNYCLGVFGLSLYTTERHLRQLFSKYFPIADVFI

Parental  VYDQQSRRSRGFAFVYFENVDDA-KEAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMGRPTYGSSRR
          .YDQQS..SRGF.FVYFEN.DDA.KE.KERANG.ELDG..I.VDFSITKRPHTPTPG.YMGRPT.GSSR.
Retrocopy AYDQQSKWSRGFVFVYFENIDDA<KETKERANGLELDGH*IGVDFSITKRPHTPTPGTYMGRPTCGSSRC

Parental  RDYYDRGYDRGYDDRDYYSRSYRGGGGGGGGWRAAQDRDQIYRRRSPSPYYSRGGYRSRSRSRSYSPRRY
          .DYYDRGYD..YDDRDYY.....GG..GGGGWRAAQDRD.I.RR.S.SPYYS.G.YRS.S.S..Y....Y
Retrocopy LDYYDRGYDQSYDDRDYYN---IGGSEGGGGWRAAQDRDLIGRRQSTSPYYSGGWYRSPS*S*AYTSCHY

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	40.55 RPM
SRP017611_kidney	0.00 RPM	47.24 RPM
SRP017611_liver	0.00 RPM	34.02 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2156 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2156 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2156 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001697	2 retrocopies	retro_btau_1245, retro_btau_850,
Canis familiaris	ENSCAFG00000013345	2 retrocopies	retro_cfam_1971, retro_cfam_966,
Cavia porcellus	ENSCPOG00000006313	1 retrocopy	retro_cpor_162,
Microcebus murinus	ENSMICG00000010611	3 retrocopies	retro_mmur_1102, retro_mmur_1135, retro_mmur_1410,
Myotis lucifugus	ENSMLUG00000005781	2 retrocopies	retro_mluc_2565, retro_mluc_2567,
Mustela putorius furo	ENSMPUG00000003157	1 retrocopy	retro_mputfur_673,
Mus musculus	ENSMUSG00000022858	6 retrocopies	retro_mmus_1187, retro_mmus_2253, retro_mmus_2313, retro_mmus_3139, retro_mmus_3617, retro_mmus_756,
Ochotona princeps	ENSOPRG00000007990	2 retrocopies	retro_opri_24, retro_opri_930,
Rattus norvegicus	ENSRNOG00000000866	1 retrocopy	retro_rnor_268,
Rattus norvegicus	ENSRNOG00000001783	4 retrocopies	retro_rnor_1130, retro_rnor_1915, retro_rnor_2156 , retro_rnor_2807,
Sarcophilus harrisii	ENSSHAG00000002437	2 retrocopies	retro_shar_684, retro_shar_826,
Ictidomys tridecemlineatus	ENSSTOG00000006720	2 retrocopies	retro_itri_1807, retro_itri_776,
Tupaia belangeri	ENSTBEG00000015927	1 retrocopy	retro_tbel_435,
Tarsius syrichta	ENSTSYG00000000388	1 retrocopy	retro_tsyr_1632,