RetrogeneDB ID: retro_opri_528

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_15225:15250..16177(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF41
• Ensembl ID: ENSOPRG00000001348
• Aliases: None
• Description: ring finger protein 41 [Source:HGNC Symbol;Acc:18401]

Sequence

>retro_opri_528
GACACGTGGAAGGACCTTATCTGCCCTATTTGCAGTGGAGTCTTGGAGGAGCCAGTATAGGCAACTCATTGCGAGCATGC
TTTCTGCAACGCCTGCATCACCCAGTGGTTCTCTCAGCAGCAGACGTGTCCGATGGACCGTAGTGTCGTGACGGTTGCCC
ACCTGCGCCCAGTGCCTCAGATCATGCGGAACATGTTGTCAAAGTCGCAGATTGCCTGGGCCAACGGTGTGCTTGGCTGT
AGTGCTCTTGTCTGACTTGACAACCTCATGTCTCAACTCAGCGACTGTGAGCACAACCCGAAGCGGCCCGTGACCTGTGA
ACAGGGCTGCGGCTTGGAGATGCCAAAGATGAGTTGCCGAACCACAACTGCGTCAAGCACCCGCGCACCTTGGTCCAGCA
GCAGCAGACAAGGCATTGCCGAACTGGAGAAGACATCCGCTGAACACAAGCACCAGCTGGCGGAGCAGAAGTCAGACATC
CAGCTGCTGAAGGCACACATGTGTGCAATACGCAGTGTCAACCCCAACCTTCAGAACCTGGAGGAGACAACTGAATACAA
CAAGATCCTAGAGTGGGTTAACTCCCTGCAGTTAGCCAGAGTGACCCGCGGAGGGGGGGGGGGGATGATCTCCACCCCTG
ACACTGTGCTCCAGGCCATCATCAAGCCCTCCCTGATAGAAAGTGGTTGCCCAGCCTCCATCGTCAATGAGCTGATTGAG
AATGCCCACGAGCGGAGCTGGCCCCAGAGTCTGGCCATCCTAGAGACGAGACAAAAGAACCGGAGCTACTACGAGAACTA
CGTGGCCAAACGCATCCCTGGCGAACAGGCTGTGGTGGTGATGACCTGTGAGAACTAGCACATGGGAGATGACATGGTGC
AGCAGCCAGGGCTTGTCATGATATTTGCACACGGTGTGGGAGAGATC

Alignment

ORF - retro_opri_528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.85 %
• Parental protein coverage: 96.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DVDEDLICPICSGVLEEPVQAPHCEHAFCNACITQWFSQQQTCPVDRSVVTVAHLRPVPRIMRNMLSKLQ
          D...DLICPICSGVLEEPV.A.HCEHAFCNACITQWFSQQQTCP.DRSVVTVAHLRPVP.IMRNMLSK.Q
Retrocopy DTWKDLICPICSGVLEEPV*ATHCEHAFCNACITQWFSQQQTCPMDRSVVTVAHLRPVPQIMRNMLSKSQ

Parental  IACDNAVFGCSAVVRLDNLMSHLSDCEHNPKRPVTCEQGCGLEMPK-DELPNHNCIKHLRTVVQQQQTR-
          IA..N.V.GCSA.V.LDNLMS.LSDCEHNPKRPVTCEQGCGLEMPK.DELPNHNC.KH.RT.VQQQQTR.
Retrocopy IAWANGVLGCSALV*LDNLMSQLSDCEHNPKRPVTCEQGCGLEMPK<DELPNHNCVKHPRTLVQQQQTR>

Parental  IAELEKTSAEHKHQLAEQKRDIQLLKAYMRAIRSVNPNLQNLEETIEYNEILEWVNSLQPARVTR--WGG
          IAELEKTSAEHKHQLAEQK.DIQLLKA.M.AIRSVNPNLQNLEET.EYN.ILEWVNSLQ.ARVTR.....
Retrocopy IAELEKTSAEHKHQLAEQKSDIQLLKAHMCAIRSVNPNLQNLEETTEYNKILEWVNSLQLARVTRGXXXX

Parental  MISTPDAVLQAVIKRSLVESGCPASIVNELIENAHERSWPQGLATLETRQMNRRYYENYVAKRIPGKQAV
          MISTPD.VLQA.IK.SL.ESGCPASIVNELIENAHERSWPQ.LA.LETRQ.NR.YYENYVAKRIPG.QAV
Retrocopy MISTPDTVLQAIIKPSLIESGCPASIVNELIENAHERSWPQSLAILETRQKNRSYYENYVAKRIPGEQAV

Parental  VVMACENQHMGDDMVQEPGLVMIFAHGVEEI
          VVM.CEN.HMGDDMVQ.PGLVMIFAHGV.EI
Retrocopy VVMTCEN*HMGDDMVQQPGLVMIFAHGVGEI

Legend:

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

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_528 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps 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 7 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,
Mus musculus	ENSMUSG00000025373	2 retrocopies	retro_mmus_3645, retro_mmus_3648,
Ochotona princeps	ENSOPRG00000001348	1 retrocopy	retro_opri_528 ,
Sarcophilus harrisii	ENSSHAG00000002679	1 retrocopy	retro_shar_38,