RetrogeneDB ID: retro_opri_1001

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5497:56866..57475(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPN1L
• Ensembl ID: ENSOPRG00000005597
• Aliases: None
• Description: poly(A) binding protein, nuclear 1-like (cytoplasmic) [Source:HGNC Symbol;Acc:37237]

Sequence

>retro_opri_1001
ATGTGGCCCTTTCTGAGCCGCAAGCTCTTCCCGCCGCCCTCTGAAACCTGGCTCCAGGTAGTCTCCTCGGACCCCAAGGC
TCAGGGCTGGGGGGCCTGGGGCAGGACTGAGAAGACCCCAGTGGGGGCTGACGCTGGGCACGGGAAGGAGCAGGAGGAGG
ACACGGAGGACGATGCCGGCCTGCTGCTGGCCCTGCTGGAGCCGGAACACCTGGCCCAGTGCCCGGTGCCTGACCAGGAG
CTGGAGGCCATCCAGCTAAAGCTGTGGGCCATGGAGCAGGCTGAGGAGGCGCCAGAGGCACCCGGAGCCAGAGGCGAGGC
TGGCCAGGAGGAGGATACACAGGCCAGCCAGCTGCTCAGCTCCGAGACCTCCGGCTGCTCCTTACCCAGGACCCCCAAGG
ACAAAGTGGAGGCTGACCACAGGTCCATCTACATGGGCAATGTGGACTCTGGGGGTACTGCCGAGGAGCTGGAGGCCTAC
TTCAACCACTGCGGCGAGATCCAGCGTGTCACCATCCTGTGCGACAAGTTCTCCAGACACCCCAAGGGCTACGGCTACAT
AGAGTTTGCCAGCGAGCGTTCTGCCCAGGCTGCCGTGGGGCTGGACGCT

Alignment

ORF - retro_opri_1001 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.58 %
• Parental protein coverage: 74.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MWPFLSRKLFPPPSETWLQVVSSDPKAQGWGAWGRTEKTPLGADAGHRKEQEEDTEDDAGLLLALLEPEH
          MWPFLSRKLFPPPSETWLQVVSSDPKAQGWGAWGRTEKTP.GADAGH.KEQEEDTEDDAGLLLALLEPEH
Retrocopy MWPFLSRKLFPPPSETWLQVVSSDPKAQGWGAWGRTEKTPVGADAGHGKEQEEDTEDDAGLLLALLEPEH

Parental  LAQCPVPDQELEAIKLKLWAMEQAEEAPQAPRAGGEAGQEEDTQASQLLSSETSGCSLPETPKDKVEADH
          LAQCPVPDQELEAI.LKLWAMEQAEEAP.AP.A.GEAGQEEDTQASQLLSSETSGCSLP.TPKDKVEADH
Retrocopy LAQCPVPDQELEAIQLKLWAMEQAEEAPEAPGARGEAGQEEDTQASQLLSSETSGCSLPRTPKDKVEADH

Parental  RSIYVGNVDYGGTAEELEAYFNHCGEIQRVTILCDKFSGHPKGYAYIEFASERSAQAAVGLDA
          RSIY.GNVD.GGTAEELEAYFNHCGEIQRVTILCDKFS.HPKGY.YIEFASERSAQAAVGLDA
Retrocopy RSIYMGNVDSGGTAEELEAYFNHCGEIQRVTILCDKFSRHPKGYGYIEFASERSAQAAVGLDA

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_1001 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 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023752	1 retrocopy	retro_btau_972,
Erinaceus europaeus	ENSEEUG00000004747	1 retrocopy	retro_eeur_633,
Ochotona princeps	ENSOPRG00000005597	2 retrocopies	retro_opri_1001 , retro_opri_174,
Tursiops truncatus	ENSTTRG00000004691	3 retrocopies	retro_ttru_1488, retro_ttru_243, retro_ttru_822,