RetrogeneDB ID: retro_ogar_3228

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873749.1:406457..407408(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000026294
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNF41
• Ensembl ID: ENSOGAG00000001525
• Aliases: None
• Description: ring finger protein 41 [Source:HGNC Symbol;Acc:18401]

Sequence

>retro_ogar_3228
ATGGGGTATGATGTAACCCGTTTCCAGGGGGAGGTTGACGAAAACCTTATCTGCTCTATTTGCAACGGCGTCTTGGAGGA
CCCAGTACAGATATCCCACTGCGAGCATGCTTTCTGCCACTCCTGTATTACCCGGTGGCTCTCTGAACAACAGACATGTC
CAGTGGACCATAGTGTTGTGACGTTTGCCCAACTGTGCCCGGTACCTCGGATTATGCGAAACATGTTGTCCAAGCTGCAG
ATTGCCTGTGACAATGCTGAGTTTGGCTGCAATGCTGTTGTTCAGCTTGATAATCTCATGTCCCACCTCAGTGACTGTGA
GCACAACCCGAACCGGCCTGTAACCTGTGAACAGGGCTGCGGCCTGGAGATGCCCCAAGAGCAGCTGCCAAACCACAATT
GCGTTAAGTACATGATCTCAGTGGTACAGCAGCAGCAGACACGCATTGCTCAGCTGGAGATGATGTCAGTGGAACACAAA
CACCAGCTGGAGGAACAGAATCAAGACATCCAGCTGCTAAAGGCATACATGCTTGCAATCCGTAGCATCAACCCCAACCT
TCAGAACCCGGAGGAGACAACTGATTATAATGAGATCCTAGAGTGGGTGGCTTCCCTTACGCCAGCAAGAGTGACCCGCT
GGGGAGGGATGATCTCAACCCCAAACTCTGTGCTCCAGGCTGTGATCAAAGAATACCTGGTGGAGAGTGGCTGCCCTGCC
TCTATTGTCAACCAGCTGATTGAAAATGCTCATGAGAGTAACTGGCCCCCTGGTCTGGCCACGCTAGAGACAAGACAGAC
GAATCGGCACTACTATGAGAACTACGTGATCAAGCGCATCCCTGGCATGCAGGCTGTTGTTGTGATGGCCTGTGAAAATC
AGCATATGGGAGAAGACATGGTGCAAGAACCAGGCCTTGTCATGACATTTTCTCATGGTGTGGAGGAGATA

Alignment

ORF - retro_ogar_3228 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGYDVTRFQGDVDEDLICPICSGVLEEPVQAPHCEHAFCNACITQWFSQQQTCPVDRSVVTVAHLRPVPR
          MGYDVTRFQG.VDE.LIC.IC.GVLE.PVQ..HCEHAFC..CIT.W.S.QQTCPVD.SVVT.A.L.PVPR
Retrocopy MGYDVTRFQGEVDENLICSICNGVLEDPVQISHCEHAFCHSCITRWLSEQQTCPVDHSVVTFAQLCPVPR

Parental  IMRNMLSKLQIACDNAVFGCSAVVRLDNLMSHLSDCEHNPKRPVTCEQGCGLEMPKDELPNHNCIKHLRS
          IMRNMLSKLQIACDNA.FGC.AVV.LDNLMSHLSDCEHNP.RPVTCEQGCGLEMP...LPNHNC.K...S
Retrocopy IMRNMLSKLQIACDNAEFGCNAVVQLDNLMSHLSDCEHNPNRPVTCEQGCGLEMPQEQLPNHNCVKYMIS

Parental  VVQQQQTRIAELEKTSAEHKHQLAEQKRDIQLLKAYMRAIRSVNPNLQNLEETIEYNEILEWVNSLQPAR
          VVQQQQTRIA.LE..S.EHKHQL.EQ..DIQLLKAYM.AIRS.NPNLQN.EET..YNEILEWV.SL.PAR
Retrocopy VVQQQQTRIAQLEMMSVEHKHQLEEQNQDIQLLKAYMLAIRSINPNLQNPEETTDYNEILEWVASLTPAR

Parental  VTRWGGMISTPDAVLQAVIKRSLVESGCPASIVNELIENAHERSWPQGLATLETRQMNRRYYENYVAKRI
          VTRWGGMISTP..VLQAVIK..LVESGCPASIVN.LIENAHE..WP.GLATLETRQ.NR.YYENYV.KRI
Retrocopy VTRWGGMISTPNSVLQAVIKEYLVESGCPASIVNQLIENAHESNWPPGLATLETRQTNRHYYENYVIKRI

Parental  PGKQAVVVMACENQHMGDDMVQEPGLVMIFAHGVEEI
          PG.QAVVVMACENQHMG.DMVQEPGLVM.F.HGVEEI
Retrocopy PGMQAVVVMACENQHMGEDMVQEPGLVMTFSHGVEEI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3228 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001320	1 retrocopy	retro_meug_901,
Meleagris gallopavo	ENSMGAG00000006916	1 retrocopy	retro_mgal_15,
Myotis lucifugus	ENSMLUG00000006057	1 retrocopy	retro_mluc_300,
Otolemur garnettii	ENSOGAG00000001525	4 retrocopies	retro_ogar_2365, retro_ogar_2487, retro_ogar_3113, retro_ogar_3228 ,
Rattus norvegicus	ENSRNOG00000023456	1 retrocopy	retro_rnor_2918,
Sarcophilus harrisii	ENSSHAG00000002679	1 retrocopy	retro_shar_38,