RetrogeneDB ID: retro_rnor_2748

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:116934378..116935458(-)
• Located in intron of: ENSRNOG00000037315

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGD1563451
• Ensembl ID: ENSRNOG00000042221
• Aliases: None
• Description: None

Sequence

>retro_rnor_2748
ATGTCAGGGGACCTGGAAGCCAAGAGCTGTGGCTACACACATATCAGTGTTCAGAAGTTCTGCTATGAGTGGACCATTAG
CAACTTTTCATTTTGCATGGACGGAATTCGTGAAAATGTTACGAGCCCAAGGTTCTCATTAGAGGCCAGTGAAGAAATGC
AATGGTGTTTGAGGATATTCCCAAATGGTGTTGATGAAGAAAGCAAAAATTACCTGTCTGTTTACCTGGGTTTGCTCAGT
TGTCCAAAGAGCCCAGTTTGGGCAAAGGTACAGTTCTGGATCATAAACGCCCAAGGAGAGAAATATCTTCTTACAAAAAT
GTCAAATGTTTTAAGGTTTCTGCTAAATCAATACTGGGGATACAAAAAGTTCATCCTTCGAGATTTCCTCCTCTCCCATA
GGCATCGACTTCTCCCTGAAGACCAGTTCACCTTGTGCTGCAAGGTGAGCATAGTAGAACGCTCCTTTAGCATGCATGGA
GATAACATGAGACCTGCAATCAAGGATCCAAGGCAGATGTTGGTCAACGACATAGGAGAGCTGTGGGAAAATTCCCTCTT
CACAGACTGCAGCCTGGTGGTAGCTGGCCAGGAATTCAGATCTCACAAGGCCATCCTAGCAGCTTGCTCTCCAGTTTTCA
GAGCCATGTTTGAACATGAAATGCTGGAGAGCCTAACAAACCGCATTGAGATCCATGACATTCACCTGCAAGTCTTTAAG
GAAATGATGGCCTTCATTTATACAGGGAAGGCACCACACCTCCACAGCCGCTCAATGGCCACAGGTTTGTTGGCAGCTGC
TGACAAGTATGACCTGCAGGGCTTGAAGGGCATGTGTGAGGATGCCTTGTGCAGGAACCTCTCTGTGAAGAATGCTGTAC
CTACTCTCATCCTGGCTGACCTCCACAAAACAGAGCACCTGAAGACTAGGGCCATGGATTTCATTATACTTCATGCTTCT
GAAGTCTCTGATAACGTGGGGTGGAAGTCAATGGTGGAGTCACATCCCCACTTGGTGGAGGAAGCATTTTACTCCCTGTC
TTCCATACAGTGTCCTGGCTTTGAGCCCTCACTCGAATGC

Alignment

ORF - retro_rnor_2748 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGDLEAKICGYTHISVQRFCYKWTISNFSFCMDGIRENITSPVFSLEGNEEVQWFLRIFPNGVDEESKD
          MSGDLEAK.CGYTHISVQ.FCY.WTISNFSFCMDGIREN.TSP.FSLE..EE.QW.LRIFPNGVDEESK.
Retrocopy MSGDLEAKSCGYTHISVQKFCYEWTISNFSFCMDGIRENVTSPRFSLEASEEMQWCLRIFPNGVDEESKN

Parental  YLSVSVGLYSCPKSPVLAKVQFWIINAQGEKHQIKEIPNILSFSPKQQWGLRKFILRDFLLSLRHWLLPE
          YLSV..GL.SCPKSPV.AKVQFWIINAQGEK.......N.L.F...Q.WG..KFILRDFLLS.RH.LLPE
Retrocopy YLSVYLGLLSCPKSPVWAKVQFWIINAQGEKYLLTKMSNVLRFLLNQYWGYKKFILRDFLLSHRHRLLPE

Parental  DQLILCCKVSVVGPSFSTPGHNMTPAKKDPRQKLADDIGELWENSLFTDCSLVVAGQEFRAHKAILAARS
          DQ..LCCKVS.V..SFS..G.NM.PA.KDPRQ.L..DIGELWENSLFTDCSLVVAGQEFR.HKAILAA.S
Retrocopy DQFTLCCKVSIVERSFSMHGDNMRPAIKDPRQMLVNDIGELWENSLFTDCSLVVAGQEFRSHKAILAACS

Parental  PVFRAMFEHEMLESLTNRVEIHDIHLQVFKEMMAFIYTGKAPHLHSHSMATDLLAAADMYDLQGLKFMCE
          PVFRAMFEHEMLESLTNR.EIHDIHLQVFKEMMAFIYTGKAPHLHS.SMAT.LLAAAD.YDLQGLK.MCE
Retrocopy PVFRAMFEHEMLESLTNRIEIHDIHLQVFKEMMAFIYTGKAPHLHSRSMATGLLAAADKYDLQGLKGMCE

Parental  DALCSNISVKNAVPTLILADLHKTEHLKTRAMDFIILHASEVSDTVGWKSMVESHPHLVEEAFYSLSSIQ
          DALC.N.SVKNAVPTLILADLHKTEHLKTRAMDFIILHASEVSD.VGWKSMVESHPHLVEEAFYSLSSIQ
Retrocopy DALCRNLSVKNAVPTLILADLHKTEHLKTRAMDFIILHASEVSDNVGWKSMVESHPHLVEEAFYSLSSIQ

Parental  CPGFEPSLEC
          CPGFEPSLEC
Retrocopy CPGFEPSLEC

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	0.07 RPM
SRP017611_kidney	0.00 RPM	0.14 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2748 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2748 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2748 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000011013	1 retrocopy	retro_mluc_2589,
Otolemur garnettii	ENSOGAG00000012793	1 retrocopy	retro_ogar_3480,
Rattus norvegicus	ENSRNOG00000004686	2 retrocopies	retro_rnor_1677, retro_rnor_534,
Rattus norvegicus	ENSRNOG00000042221	1 retrocopy	retro_rnor_2748 ,
Rattus norvegicus	ENSRNOG00000047767	2 retrocopies	retro_rnor_1675, retro_rnor_26,