RetrogeneDB ID: retro_opri_196

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3476:156000..156297(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAGE3
• Ensembl ID: ENSOPRG00000003778
• Aliases: None
• Description: L antigen family, member 3 [Source:HGNC Symbol;Acc:26058]

Sequence

>retro_opri_196
TCGCCGGCTCCACGCCTTCCAGTTCAGGGCAGAGATGTCCGGCCGCAGCCTCGTGACCCAGGAATCCGAACACATTTATT
CACCCTCGGTTGTGTCCTTCCCGACCCGTTGGGAAGTAGAAATCGCCCGGGAATCCCTGGCTCCAGATGCCGAACCCCAC
TAAGAAGCAACTGGGAAAGAAGCTGGTCGTGAGGGGCGCCATGCTGGCGGTCCGCTGGACCGCTAGAGATCCTCGCCCCC
CTCCAAGTGTCCGAAATCCACTTCGTGGAGCAGTTTTCCCTACTGGTGCGAACCCTG

Alignment

ORF - retro_opri_196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.37 %
• Parental protein coverage: 71.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  APAAHVPVPGGEVATAGSRPGMRTHFFTLS-VPFPTRLEAEIALESLAPDAEPHHEA-IGKDLAVSGTML
          .PA...PV.G..V......PG.RTH.FTL..V.FPTR.E.EIA.ESLAPDAEPH.EA..GK.L.V.G.ML
Retrocopy SPAPRLPVQGRDVRPQPRDPGIRTHLFTLG>VSFPTRWEVEIARESLAPDAEPH*EA>LGKKLVVRGAML

Parental  AVRWTAKDPR-FLRVSIINFLEQLSLVVRTL
          AVRWTA.DPR..L.VS.I.F.EQ.SL.VRTL
Retrocopy AVRWTARDPR>PLQVSEIHFVEQFSLLVRTL

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_196 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024143	1 retrocopy	retro_dnov_244,
Dipodomys ordii	ENSDORG00000009093	1 retrocopy	retro_dord_448,
Homo sapiens	ENSG00000196976	1 retrocopy	retro_hsap_4244,
Gorilla gorilla	ENSGGOG00000013507	1 retrocopy	retro_ggor_2845,
Macaca mulatta	ENSMMUG00000007739	1 retrocopy	retro_mmul_1145,
Mus musculus	ENSMUSG00000015289	2 retrocopies	retro_mmus_1411, retro_mmus_1665,
Nomascus leucogenys	ENSNLEG00000014285	1 retrocopy	retro_nleu_1373,
Ochotona princeps	ENSOPRG00000003778	2 retrocopies	retro_opri_196 , retro_opri_549,
Pongo abelii	ENSPPYG00000020881	1 retrocopy	retro_pabe_3394,
Rattus norvegicus	ENSRNOG00000037249	1 retrocopy	retro_rnor_595,
Sus scrofa	ENSSSCG00000025528	1 retrocopy	retro_sscr_94,