RetrogeneDB ID: retro_opri_828

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_34982:2913..3354(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM96A
• Ensembl ID: ENSOPRG00000015229
• Aliases: None
• Description: family with sequence similarity 96, member A [Source:HGNC Symbol;Acc:26235]

Sequence

>retro_opri_828
AGAGTCCTGTGGCTCTCAGGCTTCTCTGAACGGGGAGCTGCCAGGCAGCCCCGGATCATGGAATAGAAAGCGCTAGAGGT
TTATGATTTGATCCGAACTATCCAGGACCCAGAAAAGTCCAATACTTTGGAAGAACAGGAAGTGGTGACAGAAAGTTGCG
TGGAGGTTCAGGAGATAAATGAAGATGACTACCTGGTTGTCATCAGGTTCACACCAATAGTACCTCATTGCTCTTTGGCA
ACTCTTTTTGGGCTATGCTTAAGAGTAAAACTTCAGAGATGTTTGCCATTTAAACATTAGTTGGAGATCTACATTTCTGA
AGGAATTCACTCAACAGAAGAAGACATCAACAAGCAGATCAATGACAAAGAGCAGGTGGCCGCTGCAATGGAGAATCCCA
AAGTACGGGAAATAGTGGAACAGTGTGTCCTGGAGCCTGAC

Alignment

ORF - retro_opri_828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.63 %
• Parental protein coverage: 91.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVLWLSGFSESGAARQPRIMEEKALEVYDLIRTIRDPEKPNTLEELEVVTESCVEVQEINEDDYLVVIRF
          RVLWLSGFSE.GAARQPRIME.KALEVYDLIRTI.DPEK.NTLEE.EVVTESCVEVQEINEDDYLVVIRF
Retrocopy RVLWLSGFSERGAARQPRIME*KALEVYDLIRTIQDPEKSNTLEEQEVVTESCVEVQEINEDDYLVVIRF

Parental  TPTVPHCSLATLIGLCLRVKLQRCLPFKHKXXXXXXXXXXXXXXXXNKQINDKERVAAAMENPNLREIVE
          TP.VPHCSLATL.GLCLRVKLQRCLPFKH.................NKQINDKE.VAAAMENP..REIVE
Retrocopy TPIVPHCSLATLFGLCLRVKLQRCLPFKH*LEIYISEGIHSTEEDINKQINDKEQVAAAMENPKVREIVE

Parental  QCVLEPD
          QCVLEPD
Retrocopy QCVLEPD

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_828 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 21 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002448	1 retrocopy	retro_amel_1707,
Bos taurus	ENSBTAG00000002012	2 retrocopies	retro_btau_509, retro_btau_984,
Canis familiaris	ENSCAFG00000017035	2 retrocopies	retro_cfam_1450, retro_cfam_439,
Callithrix jacchus	ENSCJAG00000004834	1 retrocopy	retro_cjac_1751,
Equus caballus	ENSECAG00000010303	1 retrocopy	retro_ecab_364,
Erinaceus europaeus	ENSEEUG00000000854	1 retrocopy	retro_eeur_323,
Felis catus	ENSFCAG00000004178	1 retrocopy	retro_fcat_1379,
Homo sapiens	ENSG00000166797	2 retrocopies	retro_hsap_2763, retro_hsap_522,
Gorilla gorilla	ENSGGOG00000016550	2 retrocopies	retro_ggor_1921, retro_ggor_481,
Loxodonta africana	ENSLAFG00000011114	1 retrocopy	retro_lafr_758,
Macropus eugenii	ENSMEUG00000005979	2 retrocopies	retro_meug_471, retro_meug_85,
Microcebus murinus	ENSMICG00000011072	1 retrocopy	retro_mmur_233,
Myotis lucifugus	ENSMLUG00000028233	2 retrocopies	retro_mluc_578, retro_mluc_893,
Mustela putorius furo	ENSMPUG00000000605	1 retrocopy	retro_mputfur_722,
Mus musculus	ENSMUSG00000032381	1 retrocopy	retro_mmus_1919,
Nomascus leucogenys	ENSNLEG00000026932	3 retrocopies	retro_nleu_156, retro_nleu_2577, retro_nleu_667,
Ochotona princeps	ENSOPRG00000015229	5 retrocopies	retro_opri_476, retro_opri_522, retro_opri_828 , retro_opri_84, retro_opri_999,
Pongo abelii	ENSPPYG00000006544	1 retrocopy	retro_pabe_224,
Pan troglodytes	ENSPTRG00000007153	2 retrocopies	retro_ptro_1870, retro_ptro_390,
Sorex araneus	ENSSARG00000002068	3 retrocopies	retro_sara_54, retro_sara_597, retro_sara_742,
Tarsius syrichta	ENSTSYG00000004186	2 retrocopies	retro_tsyr_195, retro_tsyr_62,