RetrogeneDB ID: retro_rnor_131

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:130673867..130674614(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000049257
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Tspan7
• Ensembl ID: ENSRNOG00000003229
• Aliases: Tspan7, A15, DXS1692E, MXS1, TALLA-1, Tm4sf2
• Description: tetraspanin-7 [Source:RefSeq peptide;Acc:NP_001102285]

Sequence

>retro_rnor_131
GTGGCACTGAGGAGAATGGAGACCAAATTTGTGGCATCATGTCTCAAAATCTTCCTCCTCATCTACTCCTTTGCATTTTG
GAGCACTGGGGTTATCTTGTTGGCTTTTGGAGTCTGGGGAAAGCTTACTCTGGGCACGTATCTCTCTCTTCTTGCCAAGA
ATATTGCAGACATTCCCTTTGTGCTCATTGGAATTGGTACCATGATTATCATTTTCGGTTTATTCGGATGCTTTGCTTCA
TGCAGAGGTAGCCCATGGATGCTGAAGTTGTATTCTCTGTTTCTGTCACTGGTGTTCCTGATTGAGCTTGTTGCTAGCAT
CTCAGGGCTTCTGCTTCATCGTGAGATCAAGGACAGATTCCTGAAGATTTATACCAATGCTATACAGAACTATAACGGCA
ATGATAAGAAGAGTCAGGCAGTGGACCAGGTGCAGTATGGTCTGATGTGCTGTGGTGTGAAGAACTACAAAGACTGGAAC
GACAACCCCTACTTCCTGAATCATGGTATCCCCCAGAGTTGCTGCAAGGATGAAACTGACTGTAATCCCCCGGATCTACA
CAATCTGACCACAGCTGCCACCAAAGTTAACAAGAGAGGTTGCTATGATCTGATGATAGGTTTCTTTGAGGCAAACATGG
CAGTCATCATTGGAATGCTGTTTACAACCACATTTTCCCAGTTGATTGGCATAAGGTTGTCCTGTTGTCTGTCCCGGATC
ATCATGACCCAACGGTATAAGAGGTGT

Alignment

ORF - retro_rnor_131 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.96 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CLQLLVHPYAFYFWITGAILLAVGVWGKLTLGTYISLIAENSTNAPYVLIGTGTTIVVFGLFGCFATCRG
          CL......Y.F.FW.TG.ILLA.GVWGKLTLGTY.SL.A.N....P.VLIG.GT.I..FGLFGCFA.CRG
Retrocopy CLKIFLLIYSFAFWSTGVILLAFGVWGKLTLGTYLSLLAKNIADIPFVLIGIGTMIIIFGLFGCFASCRG

Parental  SPWMLKLYAMFLSLVFLAELVAGISGFVFRHEIKDTFLRTYTDAMQNYNGKDERSRAVDHVQRSLSCCGV
          SPWMLKLY..FLSLVFL.ELVA.ISG.....EIKD.FL..YT.A.QNYNG.D..S.AVD.VQ..L.CCGV
Retrocopy SPWMLKLYSLFLSLVFLIELVASISGLLLHREIKDRFLKIYTNAIQNYNGNDKKSQAVDQVQYGLMCCGV

Parental  QNYTNWSSSPYFLEHGIPPSCCMNETDCNPLDLHNLTVAATKVNQKGCYDLVTSFMETNMGIIAGVAFGI
          .NY..W...PYFL.HGIP.SCC..ETDCNP.DLHNLT.AATKVN..GCYDL...F.E.NM..I.G..F..
Retrocopy KNYKDWNDNPYFLNHGIPQSCCKDETDCNPPDLHNLTTAATKVNKRGCYDLMIGFFEANMAVIIGMLFTT

Parental  AFSQLIGMLLACCLSRFITANQYE
          .FSQLIG..L.CCLSR.I....Y.
Retrocopy TFSQLIGIRLSCCLSRIIMTQRYK

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	795.03 RPM
SRP017611_kidney	0.00 RPM	51.64 RPM
SRP017611_liver	0.00 RPM	52.31 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_131 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_131 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_131 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_157

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000002809	1 retrocopy	retro_meug_1563,
Mus musculus	ENSMUSG00000058254	1 retrocopy	retro_mmus_157,
Otolemur garnettii	ENSOGAG00000008547	2 retrocopies	retro_ogar_1615, retro_ogar_3124,
Rattus norvegicus	ENSRNOG00000003229	1 retrocopy	retro_rnor_131 ,