RetrogeneDB ID: retro_rnor_1737

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:38280414..38281296(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tatdn1
• Ensembl ID: ENSRNOG00000047198
• Aliases: None
• Description: TatD DNase domain containing 1 [Source:MGI Symbol;Acc:MGI:1916944]

Sequence

>retro_rnor_1737
AGTCTCTTCAAGTTCATGGATATTGGAATCAACCTGACAGATCCTATGTTCAGAGGAATTTATAGGGGGCTTCAGAAGCA
TCAAGATGATTTACAAGAGGTAATAGGGAGAGCTGTCCAGATAGGTGTTAAAAAGTTTATGATCACAGGTGGAAGTCTAC
AAGACAGTAAAGAGGCACTGCGGTTGGCACAAACATATGACAAGTTTTTCAGTACAGTGGGGTGTCATCCCATGAGATGT
GATGAGTTTGAGAAGGACAGCCCTGACCAGTACTTAGCAGGATTGCTGCACCTTGCTGAAAACAACAAAGGAAAAGTTGT
AGCAATAGGGGAGTGTGGACTTGATTTTGACCGACTTCAGTTTTGTCCCAAAGATACTCAACTCAAATATTTGAAAAACA
ATTTGAATTGTCAGAACAAACAAAATTACCAATGTTTCTTCATTGTCGAAATTCACATACTGAGTTTTTTGGATATTGTG
AGAAGATATAGAGATCGGTATGTGGGTGGAGTGGTGTATTCATTTGATGGTACGAAGGAAGCAGCGGCTGCTTTGATTGA
CTTGGACCTTTATATAGGATTTAATGGTTGCTCTCTGAAAACTGAAGCTAATTTGGAAGTTCTGAAGTCAATACCTAGTG
AAAAACTAATGATTGAGACAGATGCACCTTGATATGGAGTTAAAAGTACACATGCTGCATCAAAACACATAAAAACCGCA
TTTCCTACCAAAAAGAAGTGGAAAGCCGGGTGCTGTTTAAAAGACAGGAACAAGCCCTGCCACATAGTTCAAATATTGGA
GATAATGTCAGCAGTAAGTGAAGAAGATCCACTGGAATATGCCAACACGCTGTATAACAAAACCATTAAAATATTCTTTT
CC

Alignment

ORF - retro_rnor_1737 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.57 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLFKRYFKDIGINLTDPMFRGIYRGVQKHQDDLQDVIGRAVQIGVKKFMITGGSLQDSKDALRLAQTNDM
          SLFK..F.DIGINLTDPMFRGIYRG.QKHQDDLQ.VIGRAVQIGVKKFMITGGSLQDSK.ALRLAQT.D.
Retrocopy SLFK--FMDIGINLTDPMFRGIYRGLQKHQDDLQEVIGRAVQIGVKKFMITGGSLQDSKEALRLAQTYDK

Parental  FFSTVGCHPTRCDEFEKDSPDQYLAGLLHLAE-NKGKVVAIGECGLDFDRLQFCPKDTQLKY-FEKQFEL
          FFSTVGCHP.RCDEFEKDSPDQYLAGLLHLAE.NKGKVVAIGECGLDFDRLQFCPKDTQLKY.FEKQFEL
Retrocopy FFSTVGCHPMRCDEFEKDSPDQYLAGLLHLAENNKGKVVAIGECGLDFDRLQFCPKDTQLKY<FEKQFEL

Parental  SEQTKLPMFLHCRNSHTE-FLDIMRRNRDRCVGGVIYGPDDVTEGTKVEVDLKLTIILSSSSLKTEANLE
          SEQTKLPMFLHCRNSHTE.FLDI.RR.RDR.VGGV.Y..D...E......DL.L.I.....SLKTEANLE
Retrocopy SEQTKLPMFLHCRNSHTE>FLDIVRRYRDRYVGGVVYSFDGTKEAAAALIDLDLYIGFNGCSLKTEANLE

Parental  VLKSIPSEKLMIETDAPWCGVKSTHAGSKYIKTAFPTKKKWEAGCCLKDRNEPCHIVQILEIMSAVREED
          VLKSIPSEKLMIETDAP..GVKSTHA.SK.IKTAFPTKKKW.AGCCLKDRN.PCHIVQILEIMSAV.EED
Retrocopy VLKSIPSEKLMIETDAP*YGVKSTHAASKHIKTAFPTKKKWKAGCCLKDRNKPCHIVQILEIMSAVSEED

Parental  PLELANTLYNNTIKIFFS
          PLE.ANTLYN.TIKIFFS
Retrocopy PLEYANTLYNKTIKIFFS

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	0.72 RPM	4.10 RPM
SRP017611_kidney	1.05 RPM	4.40 RPM
SRP017611_liver	0.61 RPM	4.98 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1737 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1737 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1737 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033446	1 retrocopy	retro_btau_463,
Homo sapiens	ENSG00000147687	1 retrocopy	retro_hsap_578,
Gorilla gorilla	ENSGGOG00000015875	1 retrocopy	retro_ggor_514,
Nomascus leucogenys	ENSNLEG00000005467	1 retrocopy	retro_nleu_804,
Oryctolagus cuniculus	ENSOCUG00000017403	1 retrocopy	retro_ocun_730,
Rattus norvegicus	ENSRNOG00000047198	1 retrocopy	retro_rnor_1737 ,
Tupaia belangeri	ENSTBEG00000006179	1 retrocopy	retro_tbel_707,