RetrogeneDB ID: retro_opri_928

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_46450:3897..4560(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000008572
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GPBP1L1
• Ensembl ID: ENSOPRG00000001584
• Aliases: None
• Description: GC-rich promoter binding protein 1-like 1 [Source:HGNC Symbol;Acc:28843]

Sequence

>retro_opri_928
TCGTATACCGAAAAGCCTCCAACAGAGATTAGGGAAGAAAAGAAAGAAGACAAGGTGGAATGATTGCAGTTTGAAGAGGA
AGATTTTCCTTCTTTGAATCCAGAAACTGGCAAACAGAATCAGCCATGCAGACCCATTGGGACCCTTTCTGGAGTGTGGG
AAAACCCACCTAGTGCCAAGCAATCTTCCAAGATGTTAGTCATCAAAAAAGTTTCCAAAGAGGATCCTGCTGCTACTCTC
TGTGCTGCATTCACCTCCCCAGGATCTCACCATGCAAATGAGAACAAAGCTTCAACCATGGTTCCAAGTGTCTATAAGAC
CTTGGTTCCTACGCCTGCGCCACCTCCTTCCAAGCCCAATGCATGGAAATCTAACAGAATGGAACACAAGTCGGGCTCCC
TTTCCTCTAACCAGGAGTCTGCTTTCACCAGTCCTGTCTCTGTTACTAAGCCAGTGGTACTGGCTGGTGCTGCACTTCTA
AACTCTCCCAAAGAGAGTCCCTCCAGCACCACTCCTCCAATTGAGGTCAGCTCCTGTTGTCTGACCAAGTTGACCTACCG
AACCACTGACAGGAAGAGTGAGTTCCTGAAAACTCTAAAGGAGGATCAGAATGGAGACTTCTCAGAGAATAGAGACTGTG
ACAAACCTGAGCGTTCAGAGGAC

Alignment

ORF - retro_opri_928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.27 %
• Parental protein coverage: 50.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AFQEKPPTEIREEKKEDKVERLQFEEEDFPSLNPEAGKQNQPCRPIGTLSGVWENPPSAKQSSKMLVIKK
          ...EKPPTEIREEKKEDKVE.LQFEEEDFPSLNPE.GKQNQPCRPIGTLSGVWENPPSAKQSSKMLVIKK
Retrocopy SYTEKPPTEIREEKKEDKVE*LQFEEEDFPSLNPETGKQNQPCRPIGTLSGVWENPPSAKQSSKMLVIKK

Parental  VSKEDPAAAFSAAFTSAGSHHANGNKASTMVPSVYKNLVPKPAPPPSKPNAWKSNRMEHKSGSLSSNRES
          VSKEDPAA...AAFTS.GSHHAN.NKASTMVPSVYK.LVP.PAPPPSKPNAWKSNRMEHKSGSLSSN.ES
Retrocopy VSKEDPAATLCAAFTSPGSHHANENKASTMVPSVYKTLVPTPAPPPSKPNAWKSNRMEHKSGSLSSNQES

Parental  AFTSPVSVTKPVVLAGAALLNSPKESPSSTTPPIEISSSRLTKLTRRTTDRKSEFLKTLKDDRNGDCDKP
          AFTSPVSVTKPVVLAGAALLNSPKESPSSTTPPIE.SS..LTKLT.RTTDRKSEFLKTLK.D.NGD....
Retrocopy AFTSPVSVTKPVVLAGAALLNSPKESPSSTTPPIEVSSCCLTKLTYRTTDRKSEFLKTLKEDQNGDFSE-

Parental  EGSEDNSTPEPKEN
          ....D...PE..E.
Retrocopy --NRDCDKPERSED

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_928 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010454	1 retrocopy	retro_chof_53,
Microcebus murinus	ENSMICG00000008449	1 retrocopy	retro_mmur_164,
Myotis lucifugus	ENSMLUG00000012432	2 retrocopies	retro_mluc_211, retro_mluc_834,
Mus musculus	ENSMUSG00000034042	2 retrocopies	retro_mmus_1391, retro_mmus_405,
Oryctolagus cuniculus	ENSOCUG00000017939	1 retrocopy	retro_ocun_427,
Otolemur garnettii	ENSOGAG00000004134	1 retrocopy	retro_ogar_1859,
Ochotona princeps	ENSOPRG00000001584	1 retrocopy	retro_opri_928 ,
Rattus norvegicus	ENSRNOG00000037595	1 retrocopy	retro_rnor_390,
Ictidomys tridecemlineatus	ENSSTOG00000013491	1 retrocopy	retro_itri_243,