RetrogeneDB ID: retro_rnor_1516

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:107462463..107462880(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ap2s1
• Ensembl ID: ENSRNOG00000015865
• Aliases: Ap2s1, Ap17
• Description: AP-2 complex subunit sigma [Source:UniProtKB/Swiss-Prot;Acc:P62744]

Sequence

>retro_rnor_1516
ATGATCCGATTCATCCTCATCCAGAACCGGGCAGGCAAGACACGCCTGGCCAAGTAATATATGCAGTTCGATGATGATGA
GAAGTAGAAGTTGATTGAGGAAGTGTACGCCGTGGTCAACATTAGGAATGCCAACCACACCAACTTTATGGAGTTCCGGA
CCTTCAAGATCATCTACTGGCGCTACACTGGCCTCTACTTCTGCATCTGCCTGGACATCAACCACAACAATCTGGCCTAT
CGTGAGGCCATACACAACTTCGTAGAAGTGATAAATGAATACTTCCACAATGTCTGTGAAATAGACCTGGTGTTCAACTT
CTACAAGGTTTACAAGGTGGTAGATGAAATGTTCCTGGCAGGAGAGATCCGAGAGACTAGCCAGATGAAGGTGCTGAAGC
AGCTGCTGAAGCTGCAG

Alignment

ORF - retro_rnor_1516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.61 %
• Parental protein coverage: 97.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCIC
          MIRFILIQNRAGKTRLAK.YMQFDDDEK.KLIEEV.AVV..R.A.HTNF.EFR.FKIIY.RY.GLYFCIC
Retrocopy MIRFILIQNRAGKTRLAK*YMQFDDDEK*KLIEEVYAVVNIRNANHTNFMEFRTFKIIYWRYTGLYFCIC

Parental  VDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQ
          .D.N.NNLAY.EAIHNFVEV.NEYFHNVCE.DLVFNFYKVY.VVDEMFLAGEIRETSQ.KVLKQLL.LQ
Retrocopy LDINHNNLAYREAIHNFVEVINEYFHNVCEIDLVFNFYKVYKVVDEMFLAGEIRETSQMKVLKQLLKLQ

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	65.86 RPM
SRP017611_kidney	0.00 RPM	66.29 RPM
SRP017611_liver	0.00 RPM	24.88 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1516 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1516 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008394	1 retrocopy	retro_amel_409,
Macropus eugenii	ENSMEUG00000001062	2 retrocopies	retro_meug_1156, retro_meug_1993,
Mus musculus	ENSMUSG00000008036	1 retrocopy	retro_mmus_2739,
Rattus norvegicus	ENSRNOG00000005765	1 retrocopy	retro_rnor_2200,
Rattus norvegicus	ENSRNOG00000015865	2 retrocopies	retro_rnor_1030, retro_rnor_1516 ,
Tursiops truncatus	ENSTTRG00000012548	1 retrocopy	retro_ttru_924,