RetrogeneDB ID: retro_rnor_1568

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:211028595..211029498(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Senp2
• Ensembl ID: ENSRNOG00000001773
• Aliases: None
• Description: Sentrin-specific protease 2 [Source:UniProtKB/Swiss-Prot;Acc:Q9EQE1]

Sequence

>retro_rnor_1568
ATGTACAGATGGCTGACTAAGGTTCTCGGCACCATTCTTCGCTGGTGTGAGCGCCCCGCGCCCCGGGCCCAGGCCCTGCT
CAAGAGGCGGCGCTCCATCAGCTCTCTGTTTTCTACTGCAGTGGACACTGATGAAATCCCAGCTAAAAGACCAAGACTAG
ATTGCTTCACTCACCAAGCAAAGAACAGTCTCTACAATGAGGCCAGCTTATTTGGATTCCCATTCCAGCTGACCACCAAA
CCCATGGTGTCTTCTGCTTGTAATGGAACACGGAATGCGGCCCCTTCAGGAGAGGTATTCTCGAACTCTCCCTCTTGTGA
ACTGATGAGTTCTGGATCCTGCAGCAGCATGCTGAAGCTGGGTAATAAATCTCCTAATGGAATACGTGACTATCCAGAGA
TCAGAGTGACAGTGGCCCGAGATCAGCCACGGAGAGTCCTGCCTTCCTTTGGTTTTACATTGAAATCAGAAGGCTATAAT
AGACCAAATGGCCGTCGCCATAGCAAAAGCAATCCAGAGAGTTCCTTAACGTGGAAACCTCAGGAGCAAGGTGTAACAGA
GATGATTTCTGAAGAGGGTGGCAAGGGTGCGAGACGTCCCCAATGCACCGTGGAGGGTGGTGTCCAGAAGGACGAAAGAG
AAAAATACCTAAAGCTATTGGAGCGTCTTAAAGAAGGTGCTCACGAAAGCACTTTTCCTCCTGCAGTTTCACATCATAGT
TCTCAGAGAATTCAGATGGACACATTAAAGACCAAAGGCTGGATGGAGGAGCAGAATCATGGAGTCAGAACAACCCATTT
TGTTCCAAAACAGTATAGAGTTGTTGAAACAAGAGGACCTATCTGTTCAGTGAGAAGTGACAAGAGGTATTTAAAAGAAA
AAGCTGACACAGAGAAGGTGGTG

Alignment

ORF - retro_rnor_1568 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.05 %
• Parental protein coverage: 51.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYRWLTKVLGTILRLCERPAPGARALLKRRRSSSSLFSTAVDTDEIPAKRPRLDCFIHQVKNSLYNAASL
          MYRWLTKVLGTILR.CERPAP.A.ALLKRRRS.SSLFSTAVDTDEIPAKRPRLDCF.HQ.KNSLYN.ASL
Retrocopy MYRWLTKVLGTILRWCERPAPRAQALLKRRRSISSLFSTAVDTDEIPAKRPRLDCFTHQAKNSLYNEASL

Parental  FGFPFQLTTKPMVSSACNGTRNVAPSGEVFSNSPSCELTTSGSCSSMLKLGNKSPNGISDYPKIRVTVAR
          FGFPFQLTTKPMVSSACNGTRN.APSGEVFSNSPSCEL..SGSCSSMLKLGNKSPNGI.DYP.IRVTVAR
Retrocopy FGFPFQLTTKPMVSSACNGTRNAAPSGEVFSNSPSCELMSSGSCSSMLKLGNKSPNGIRDYPEIRVTVAR

Parental  DQPRRVLPSFGFTLKSEGYNRRPSGRRHSKSNPESSLPWKPQEQGVTEMISEEGGKGARRPHCTVEEGVQ
          DQPRRVLPSFGFTLKSEGYNR.P.GRRHSKSNPESSL.WKPQEQGVTEMISEEGGKGARRP.CTVE.GVQ
Retrocopy DQPRRVLPSFGFTLKSEGYNR-PNGRRHSKSNPESSLTWKPQEQGVTEMISEEGGKGARRPQCTVEGGVQ

Parental  KDEREKYLKLLERLKEGAHGSTFPPAVSHHSSQRTQMDTLKTKGWMEEQNHGVRTTHLVPKQYRVVETRG
          KDEREKYLKLLERLKEGAH.STFPPAVSHHSSQR.QMDTLKTKGWMEEQNHGVRTTH.VPKQYRVVETRG
Retrocopy KDEREKYLKLLERLKEGAHESTFPPAVSHHSSQRIQMDTLKTKGWMEEQNHGVRTTHFVPKQYRVVETRG

Parental  PLCSVRSEKRYSKGKADTEKVV
          P.CSVRS.KRY.K.KADTEKVV
Retrocopy PICSVRSDKRYLKEKADTEKVV

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	72.11 RPM
SRP017611_kidney	0.00 RPM	28.05 RPM
SRP017611_liver	0.00 RPM	14.59 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1568 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1568 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1568 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011230	1 retrocopy	retro_ecab_586,
Rattus norvegicus	ENSRNOG00000001773	1 retrocopy	retro_rnor_1568 ,
Rattus norvegicus	ENSRNOG00000048136	2 retrocopies	retro_rnor_1522, retro_rnor_531,
Tursiops truncatus	ENSTTRG00000008239	1 retrocopy	retro_ttru_377,