RetrogeneDB ID: retro_rnor_1642

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:134993054..134993948(-)
• Located in intron of: ENSRNOG00000049136

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSRNOG00000047601
• Aliases: None
• Description: None

Sequence

>retro_rnor_1642
GGGAATCATTCTGCAGCAGTTGTGTTCATCTTGGTGGGATTAACCCAGCAGCCTGGGCTCCTGCTGCCCCTCTTCCTTCT
GTTCCTGAGCATCTAAGTGGTGACAGCAGTGGGGAATCTGGGCATGATCCTGCTCATCTCAGTCAGCCCACTTCTGCACA
CTCCCATGTACTATTTCCTCAGCAGTTTATCCTTTGTTGATCTCTGCTATTCCACTGCCATTACACCCAAAATGCTGGTG
AACTTCCTTGGGAAGAAAAATATGATTGTCTATTCAGAGTGCATGGCCCAGCTCTTTTTCTTTGTAATCTTTGTGGTGGC
CGAGGGTTACCTCCTGACTGCCATGGCATATGATCGCTATGTGGCCATCTGCAGACCATTGCTCTATAATGTGATGATGT
CCCCTAGACTCTGCTCACTGCTAGTACTGGTTGCTTTCATCTTAGGCTTTATGTCAGCTTTAGCACACACAAGTGCTATG
ATGAATCTGAGCTTCTGTAAATCGTACATCATAAGCCATTATTTCTGTGATGTTCTTCCCCTCCTAAACCTCTCCTGCTC
TGACACAAAGCTGAATGAGCTTCTCCTATTTATCATTGCAGGCTTCAACACCTTGGTGCCTACACTAGCTGTTGCCATCT
CCTATATCTTCATATTCTGCAGCATCATTCATATCAGCTCATCAGAGGGCAGGTCCAAAGCATTTGGAACCTGCAGCTCT
CATCTCATGGCTGTGGGGATCTTCTTTGGGTCTATCACCTTTATGTATTTTAAGCCTCCTTCAAGTAACTCCCTGCAGCA
AGAGAAGGTGTCTTCTGTGTTCTATACCACAGTAATCCCCATGCTGAACCCATTAATATATAGTTTGAGGAACAAAGATG
TGAAGAAATCATTG

Alignment

ORF - retro_rnor_1642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNHSAVVVFVLVGLTKQPELLLPLFFLFLVIYVLTVVGNLGMILLIIVSSVPLLHTPMYYFLSSLSFVDL
          GNHSA.VVF.LVGLT.QP.LLLPLF.LFL.I.V.T.VGNLGMILLI.VS..PLLHTPMYYFLSSLSFVDL
Retrocopy GNHSAAVVFILVGLTQQPGLLLPLFLLFLSI*VVTAVGNLGMILLISVS--PLLHTPMYYFLSSLSFVDL

Parental  CYSTAITPKMLVNFLGKKNMIVYSECMAQLFFFVIFVVAEGYLLTAMAYDRYVAICRPLLYNVMMSPRLC
          CYSTAITPKMLVNFLGKKNMIVYSECMAQLFFFVIFVVAEGYLLTAMAYDRYVAICRPLLYNVMMSPRLC
Retrocopy CYSTAITPKMLVNFLGKKNMIVYSECMAQLFFFVIFVVAEGYLLTAMAYDRYVAICRPLLYNVMMSPRLC

Parental  SLLVLVAFILGFMSALAHTSAMMNLSFCKSYIISHYFCDVLPLLNLSCSDTKLNELLLFIIAGFNTLVPT
          SLLVLVAFILGFMSALAHTSAMMNLSFCKSYIISHYFCDVLPLLNLSCSDTKLNELLLFIIAGFNTLVPT
Retrocopy SLLVLVAFILGFMSALAHTSAMMNLSFCKSYIISHYFCDVLPLLNLSCSDTKLNELLLFIIAGFNTLVPT

Parental  LAVAISYIFIFCSIIHISSSEGRSKAFGTCSSHLMAVGIFFGSITFMYFKPPSSNSLQQEKVSSVFYTTV
          LAVAISYIFIFCSIIHISSSEGRSKAFGTCSSHLMAVGIFFGSITFMYFKPPSSNSLQQEKVSSVFYTTV
Retrocopy LAVAISYIFIFCSIIHISSSEGRSKAFGTCSSHLMAVGIFFGSITFMYFKPPSSNSLQQEKVSSVFYTTV

Parental  IPMLNPLIYSLRNKDVKKSL
          IPMLNPLIYSLRNKDVKKSL
Retrocopy IPMLNPLIYSLRNKDVKKSL

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_1642 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1642 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1642 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000045971	3 retrocopies	retro_rnor_2562, retro_rnor_375, retro_rnor_376,
Rattus norvegicus	ENSRNOG00000047601	6 retrocopies	retro_rnor_1493, retro_rnor_1641, retro_rnor_1642 , retro_rnor_2563, retro_rnor_2564, retro_rnor_2622,
Rattus norvegicus	ENSRNOG00000049226	1 retrocopy	retro_rnor_1811,