RetrogeneDB ID: retro_rnor_1675

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:210500530..210501337(-)
• Located in intron of: ENSRNOG00000047767

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSRNOG00000047767
• Aliases: None
• Description: None

Sequence

>retro_rnor_1675
ATGACAGGGGACCTGGAAGCCAAGATCTGTGGCTTCACACATATCAGTGTTCAGAATTTCTCCTATGAATGGACCATTAG
CAACTTTTCATTTTGCATGGATGGAATTTGGAAAATTATTACAAGCCCAGTGTTCTCATTAGAGGCCAATGAAGAAGTAC
AATGGTGTTTGAGAATATACCCAAACGGTGTTAATGAAGAAAGCAAAGATTATCTGTCTGTTTCCCTGGGTTTGCTCAAT
TGTCCAAAGAGCCCAGTTTTGGCAAAGTTGCAGTTCTGGATCATAAATGCCCAAGGAGAGAAACATCAAATTACAAAGAA
CCCAAATGTTTTAAGGTTTCCTCCAAATGAACAATGGGGATTGAGAAAGTTTATCCTTCGAGATTTCCTCCTTTCCCATA
GGCATTGGCTTCTCCCTGAAGAACAGCTCATTCTGTGTTGCAAGGTATCCATTGTAGGACCCTGCTTTAGCAGGCCTGGA
CAAAACATGACACCTGCAATCAAGGATCCAACACAGATGTTGGCGGATGATGTAGGAGAGCTGTGGGAAAATTCCCTCTT
CACAGACTGCAGTCTGGTTGTAGGTGGTCAGGAATTCAGAGCTCACAAGGCCATTGTAGCAGCTCACTCTCCAGTTTTCA
GAGCCATGTTTGAACATGAAATGCAGGAGCGCCTAACAAACTGCATTGAGATCCATGACATTCATCTGCAAGTCTTTAAG
GAAATGATGGCTTTCATTTACACAGGGAAGGCACCACACCTCCACAGCCACTCAATGGCCACTGGTTTGTTGGCAGCTGC
TGACATG

Alignment

ORF - retro_rnor_1675 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.73 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGDLEAKISGYTHISVQRFCYKWTISNFSFCMDGIRENITSPVFSLEGNEEVQWCLRIFPNGVDEESKD
          M.GDLEAKI.G.THISVQ.F.Y.WTISNFSFCMDGI...ITSPVFSLE.NEEVQWCLRI.PNGV.EESKD
Retrocopy MTGDLEAKICGFTHISVQNFSYEWTISNFSFCMDGIWKIITSPVFSLEANEEVQWCLRIYPNGVNEESKD

Parental  YLSVSLGLHSCPKSPVLAKVQFWIINAQGEKYLITKISNVLKFLPNQYWGYKKFILRDFLLSHRHWLLPE
          YLSVSLGL..CPKSPVLAK.QFWIINAQGEK..ITK..NVL.F.PN..WG..KFILRDFLLSHRHWLLPE
Retrocopy YLSVSLGLLNCPKSPVLAKLQFWIINAQGEKHQITKNPNVLRFPPNEQWGLRKFILRDFLLSHRHWLLPE

Parental  EQLILCCKVSIIGPCFSRPGQNMTPAIKDPRQILADDVGELWENSLFTDCSLVVAGQEFRAHKAILAGHS
          EQLILCCKVSI.GPCFSRPGQNMTPAIKDP.Q.LADDVGELWENSLFTDCSLVV.GQEFRAHKAI.A.HS
Retrocopy EQLILCCKVSIVGPCFSRPGQNMTPAIKDPTQMLADDVGELWENSLFTDCSLVVGGQEFRAHKAIVAAHS

Parental  PVFRAMFEHEMQERLTNRIEFHDIHLQVFKEMMAFIYTGKAPHLHSHSMATGLLAAADM
          PVFRAMFEHEMQERLTN.IE.HDIHLQVFKEMMAFIYTGKAPHLHSHSMATGLLAAADM
Retrocopy PVFRAMFEHEMQERLTNCIEIHDIHLQVFKEMMAFIYTGKAPHLHSHSMATGLLAAADM

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 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_1675 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1675 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,