RetrogeneDB ID: retro_rnor_2197

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:17083978..17084589(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tiprl
• Ensembl ID: ENSRNOG00000003048
• Aliases: Tiprl, RGD1310442
• Description: TIP41-like protein [Source:UniProtKB/Swiss-Prot;Acc:A2VCX1]

Sequence

>retro_rnor_2197
GAGTTCAATGCTACAGATGCACTGAGATGTGTGAACAACTACCAGGGCATGCTCAAAGTAGCTTGTGCTGAAGAGTGACA
GGAAAGAAGAACGGAGGGTGAACATTCCAAAGAAGCTACTAAACCATGTGACTGGACCTATACAACAGATTATAAAGAGT
CATTGCTTGGAGAATCTCTTAAGTTAAAGGTTGTACCTACAACAGATCATATAGATACAGAAACATTGAAAGCCAGAAAC
AGATAAAATTTTTTGAAGAAGTTCTCCCTTTTGAGGATGAATTGCATGATCACAGAGTTTCCAGCCGGAGTGTGAAAATT
CGAGTAATGCCTTCCAGCTTTTTTTCTGCTACTGCGGTTTTTCCTCAGAAAAAAACTGATGGGGCGCTCATCCGAACAAA
TGACACAAGGCTTTACCATGAAACTGACAAGACCTACATGTTACGACGATATACATCCAGAGAGAGCAAAATTGCTAATT
TAATGCATGTCCCATCTTCCCTCTTCACAGAACCTAACGAAATAGCACAGTATTTACCAATTAAGGAAGCAGTTTGTGAG
AAGCTAGTATTTCCAGAAAGAACTGATCTTAATCCTGCGCCCTCAGAATCA

Alignment

ORF - retro_rnor_2197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.9 %
• Parental protein coverage: 74.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EFNATDALRCVNNYQGMLKVACAEEWQESRTEGEHSKEVIKPYDWTYTTDYKGTLLGESLKLKVVPTTDH
          EFNATDALRCVNNYQGMLKVACAEE.QE.RTEGEHSKE..KP.DWTYTTDYK..LLGESLKLKVVPTTDH
Retrocopy EFNATDALRCVNNYQGMLKVACAEE*QERRTEGEHSKEATKPCDWTYTTDYKESLLGESLKLKVVPTTDH

Parental  IDTEKLKAR-EQIKFFEEVLLFEDELHDHGVSSLSVKIRVMPSSFFLLLRFF--LRIDGVLIRMNDTRLY
          IDTE.LKAR..QIKFFEEVL.FEDELHDH.VSS.SVKIRVMPSSFF.....F.....DG.LIR.NDTRLY
Retrocopy IDTETLKAR<KQIKFFEEVLPFEDELHDHRVSSRSVKIRVMPSSFFSATAVFPQKKTDGALIRTNDTRLY

Parental  HEADKTYMLREYTSRESKIANLMHVPPSLFTEPNEISQYLPIKEAVCEKLVFPERIDPNPVDSES
          HE.DKTYMLR.YTSRESKIANLMHVP.SLFTEPNEI.QYLPIKEAVCEKLVFPER.D.NP..SES
Retrocopy HETDKTYMLRRYTSRESKIANLMHVPSSLFTEPNEIAQYLPIKEAVCEKLVFPERTDLNPAPSES

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	20.92 RPM
SRP017611_kidney	0.00 RPM	19.33 RPM
SRP017611_liver	0.00 RPM	7.53 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2197 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2197 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2197 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008689	3 retrocopies	retro_chof_1079, retro_chof_1094, retro_chof_1746,
Cavia porcellus	ENSCPOG00000009945	1 retrocopy	retro_cpor_763,
Echinops telfairi	ENSETEG00000005808	1 retrocopy	retro_etel_1273,
Microcebus murinus	ENSMICG00000007808	1 retrocopy	retro_mmur_1335,
Myotis lucifugus	ENSMLUG00000011927	3 retrocopies	retro_mluc_607, retro_mluc_909, retro_mluc_941,
Monodelphis domestica	ENSMODG00000002880	1 retrocopy	retro_mdom_180,
Mus musculus	ENSMUSG00000040843	1 retrocopy	retro_mmus_2653,
Ochotona princeps	ENSOPRG00000011313	1 retrocopy	retro_opri_885,
Pteropus vampyrus	ENSPVAG00000005071	1 retrocopy	retro_pvam_257,
Rattus norvegicus	ENSRNOG00000003048	1 retrocopy	retro_rnor_2197 ,
Sarcophilus harrisii	ENSSHAG00000018932	1 retrocopy	retro_shar_771,
Ictidomys tridecemlineatus	ENSSTOG00000014921	1 retrocopy	retro_itri_1756,
Tupaia belangeri	ENSTBEG00000017081	3 retrocopies	retro_tbel_1717, retro_tbel_2833, retro_tbel_3376,