RetrogeneDB ID: retro_opri_714

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_253:170435..170828(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000004149
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBL4A
• Ensembl ID: ENSOPRG00000012645
• Aliases: None
• Description: ubiquitin-like 4A [Source:HGNC Symbol;Acc:12505]

Sequence

>retro_opri_714
ATGTTACTCACAGTCAAGCTTCTCCTGGGCCGGCGATGCAGTGTGAAGGTGTCGGGGCAAGAGAGTGTGGCCGCACTGAA
GAAGCTGGTGTCACAGCAGCTACAGGTGCCTGAGGAGCAGCAGCACCTGCTGTTTCGTGGCCAGCTCCTGGCAGATGACA
AGTGCCTCTCGGATTACTGCATTGGGCCCAATGCCTCCATCAACGTCATTGTGCGGCCCCTGGAGAAGATAGAGCTGGAG
AACGCTCACCAGCCCCAGCCCCAGCCCCTGTGGCAGCAGCTGGACCGGGTCCTGGCCAGACACTTTGGGCTGCAGGATGC
CAAGGCTGTGCTGCAGCTGCTGAGACAAGAGCATGAGGGGCGCCTGCAGAGGGTAAGCCTACAGGACCTGGAG

Alignment

ORF - retro_opri_714 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQLTVKALQGRECSLQVPEDEQVSTLKQLVSERLNVPVHQQRLLFKGKALADGKRLSDYSIGPNSKLNLV
          M.LTVK.L.GR.CS..V...E.V..LK.LVS..L.VP..QQ.LLF.G..LAD.K.LSDY.IGPN...N..
Retrocopy MLLTVKLLLGRRCSVKVSGQESVAALKKLVSQQLQVPEEQQHLLFRGQLLADDKCLSDYCIGPNASINVI

Parental  VKPLEKVVL--AADSPPPPVWQLISKVLARHFSAADASRVLEQLQRDYERSLSRLTLDDIE
          V.PLEK..L..A........WQ....VLARHF...DA..VL..L....E..L.R..L.D.E
Retrocopy VRPLEKIELENAXXXXXXXXWQQLDRVLARHFGLQDAKAVLQLLRQEHEGRLQRVSLQDLE

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_714 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005040	1 retrocopy	retro_acar_123,
Bos taurus	ENSBTAG00000014331	1 retrocopy	retro_btau_195,
Callithrix jacchus	ENSCJAG00000016805	1 retrocopy	retro_cjac_3272,
Ochotona princeps	ENSOPRG00000012645	1 retrocopy	retro_opri_714 ,
Rattus norvegicus	ENSRNOG00000037250	1 retrocopy	retro_rnor_2789,