RetrogeneDB ID: retro_mmus_3208

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:65278752..65279229(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpl24
• Ensembl ID: ENSMUSG00000022601
• Aliases: Zbtb11, 9230110G02Rik, ZNF-U69274
• Description: ribosomal protein L24 [Source:MGI Symbol;Acc:MGI:1915443]

Sequence

>retro_mmus_3208
ATGAAAGTCAAGCTGTGCACTTTCGGGGGAGCAGAGAGGGGCAAGATCTACCCCAGACACAGGCAGCACTATACCACGAC
CAACTGGAAGGTTTTCCAGTTTCTTAATACAAAATACAAGTCTGCGATTCCTTTCCAAACGGAATCCTCAGCAGTTAAAC
TATACTGTACTCTACAGAAAGGACAGTCAAGGGAAATTCCATAGAAAAGAACCTGTCAAGCCAGCTGTCAAATTCCAGGG
AGCTGTCACTGATGCATCTCTTGCTGGTATAATGGTCAAGAGGAATCAGAAACTAGAAGTTAGGAAAGCTCAGGGAGAGC
AAGCTCTAAGGGCTGCCAAGGAAGCAAAAGAGGCTAAGCAGGCATCGAAGAAGACAGCAATGAGGGTGCCAAGGCCCTCA
CAAAGACAGTACCTAGACAAGCAAATAAACACATAATGAAGACTGTGAGGATCTCTGTTCCCGGAGTTGGTGGGAAA

Alignment

ORF - retro_mmus_3208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.59 %
• Parental protein coverage: 99.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKVELCSFSGY---KIYPGHGRRYARTDGKVFQFLNAKCESA-FLSKRNPRQINWTVLYRRKHKKGQSEE
          MKV.LC.F.G....KIYP.H...Y..T..KVFQFLN.K..SA.FLSKRNP.Q.N.TVLYR...K..Q...
Retrocopy MKVKLCTFGGAERGKIYPRHRQHYTTTNWKVFQFLNTKYKSA>FLSKRNPQQLNYTVLYR---KDSQGKF

Parental  IQKKRTRRAVKFQRAITGASLADIMAKRNQKPEVRKAQREQAIRAAKEAKKAKQASKKTAM-AAAKAPTK
          ..K.....AVKFQ.A.T.ASLA.IM.KRNQK.EVRKAQ.EQA.RAAKEAK.AKQASKKTAM...AKA.TK
Retrocopy HRKEPVKPAVKFQGAVTDASLAGIMVKRNQKLEVRKAQGEQALRAAKEAKEAKQASKKTAM<EGAKALTK

Parental  AAPKQ---KIVKPVKVSAPRVGGK
          ..P.Q....I.K.V..S.P.VGGK
Retrocopy TVPRQANKHIMKTVRISVPGVGGK

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
SRP007412_brain	0.00 RPM	83.94 RPM
SRP007412_cerebellum	0.00 RPM	81.85 RPM
SRP007412_heart	0.00 RPM	59.33 RPM
SRP007412_kidney	0.00 RPM	59.77 RPM
SRP007412_liver	0.00 RPM	60.76 RPM
SRP007412_testis	0.00 RPM	67.05 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3208 was not detected

EST

No EST(s) were mapped for retro_mmus_3208 retrocopy.

TSS

No TSS is located nearby retro_mmus_3208 retrocopy 5' end.

Lab

retro_mmus_3208 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3208 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000022601	13 retrocopies	retro_mmus_1398, retro_mmus_1418, retro_mmus_1555, retro_mmus_2145, retro_mmus_2429, retro_mmus_2434, retro_mmus_2870, retro_mmus_2981, retro_mmus_3208 , retro_mmus_3384, retro_mmus_500, retro_mmus_793, retro_mmus_87,