RetrogeneDB ID: retro_opri_953

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_496:146748..147152(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP30L
• Ensembl ID: ENSOPRG00000014552
• Aliases: None
• Description: SAP30-like [Source:HGNC Symbol;Acc:25663]

Sequence

>retro_opri_953
AAGGACGGTGTATGGTGCAGCCAGGGGACAGGCAATGTCAACTTCAGCAAGAGGATCCAGAAGGGCATCTCCCAGAAGAA
AGTCAAGACCGAACTGGATAAATGCCCAAGGCATCTTTAATTTGTGGTTATCAAAAATTTTAAACTCTGAATGTTTGGGA
AAGAAAGAAAAAACAAGTGATAATGATGGAGGTGATTCACCTGTTCAAAATAATGATACTCCAGAGGTTGATTTATACCA
ACTACTAGTAAATACACTTAAGAGATACAAAAGATACTTCAAGCTACCAACCAGACCAGGACTTAATAAAACACAACTTG
AGATAGTCATCTGCCACTTTAGGTCTATTCTAGTTGAATGAAAAGGACACCTTAATATATTTCATTCACTCAGTGAAGAA
TGAC

Alignment

ORF - retro_opri_953 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.68 %
• Parental protein coverage: 76.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EDGERCVRPAGNASFSKRVQKSISQKKLKLDIDKSVRHL-YICDFHKNFIQSVRNKRKRK-TSDDGGDSP
          .DG..C....GN..FSKR.QK.ISQKK.K...DK..RHL..IC...K.....V....K......DGGDSP
Retrocopy KDGVWCSQGTGNVNFSKRIQKGISQKKVKTELDKCPRHL<LICGYQKF*TLNVWERKKKQ<SDNDGGDSP

Parental  EHDTDIPEVDLFQLQVNTLRRYKRHYKLQTRPGFNKAQLAETVSRHFRNIPV-NEKETLAYFIYMVKSN
          ....D.PEVDL.QL.VNTL.RYKR..KL.TRPG.NK.QL.E.V..HFR.I.V.NEK.TL.YFI..VK..
Retrocopy VQNNDTPEVDLYQLLVNTLKRYKRYFKLPTRPGLNKTQL-EIVICHFRSILV>NEKDTLIYFIHSVKND

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_953 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
Ailuropoda melanoleuca	ENSAMEG00000016695	1 retrocopy	retro_amel_588,
Bos taurus	ENSBTAG00000004000	1 retrocopy	retro_btau_1024,
Canis familiaris	ENSCAFG00000017642	1 retrocopy	retro_cfam_2138,
Felis catus	ENSFCAG00000014985	1 retrocopy	retro_fcat_1968,
Mustela putorius furo	ENSMPUG00000013575	1 retrocopy	retro_mputfur_955,
Ochotona princeps	ENSOPRG00000014552	2 retrocopies	retro_opri_176, retro_opri_953 ,