RetrogeneDB ID: retro_opri_678

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_23589:50963..51922(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WBP11
• Ensembl ID: ENSOPRG00000015008
• Aliases: None
• Description: WW domain binding protein 11 [Source:HGNC Symbol;Acc:16461]

Sequence

>retro_opri_678
AAAGAATTGAGAAAACTAGAAGTGAACAGAAACAAAAAAGGGATCAGCTTAGCCAGTATTTTGATGCTGTTAAGAACGCA
TGTGGACATGGAGAGTATTCCCTTGCCAGATATACCACATGCTCCTTCCAACATCTTGATCCAGGACATTGCACTTCCTG
GTGTCCAGCCATCCTCCATTCTTAAGAAAACTTCAGCCTATAGACCTCCACCCAAGGCAGTTTCTATAATTCATCTTCTT
GGACATGGTGTTCCACATTTGTCCCCCTGACAGAAAACCTCCTGGCCCTCCCTCTGGTCCGTTGCCACTCCAGGTCTTGC
AGATGTATGGCTGCAAAGTGGACTTTGCCCTGTGTTTTCCCCCTTGTAGGCGGGATCTTCATCATGCTGTATAGTCCTGA
ACTTGTTCAGCGAGGTCATGATAAGGATGTTCCCAGCACGAGTGAAGATTATGGCTATCCTGAGGGCATGGATCAGGATA
AACATGATGACAGCACCAATGGTAGTGACACTGACAGATCAGATGGAGAAAGTGATGGGGATGAATTCGTGCATTGTGGT
GACAGTGAATGAGACAACAATGAAGAAAACAAATCAGGTCTGAGTGTAGGATTTGCTGATATGCCTGGAAAATCGAGGAA
GAAAGAGAAGAACATGAAAGAGTTGATCCCTCTTAAAGCCATGATGCTCCGAATGGCAGGTCAGAAACTCCCTGAGGAGG
GAAGAGAAGTAGAGGAATTTTCCGAGGATGATGATGAAGATGATTCTGCAGCAGAAAAGCAATCACACAAACAACGTAAA
GAAGATTCCCATTCTGATGGTACATCTGCATCCTCAAAGCAGCAGACTCCTCCTCCCCAATCTGTTCCTTCCTCTCAGAC
TCAAGCACCTCCCATGCCAGGACCCCCTCCTACTGACCCACCACCTGCTCTGCCTTTACCACCTCCTGGAACACCTACC

Alignment

ORF - retro_opri_678 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.31 %
• Parental protein coverage: 50.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KELRKLEVEYEQKRAQLSQYFDAVKNAQHVEVESIPLPDMPHAPSNILIQDIPLPGAQPPSILKKTSAYG
          KELRKLEV....K...L...........HV..ESIPLPD.PHAPSNILIQDI.LPG.QP.SILKKTSAY.
Retrocopy KELRKLEVNRNKKGISLASILMLLRT--HVDMESIPLPDIPHAPSNILIQDIALPGVQPSSILKKTSAYR

Parental  PTTRAVSIFPLLGHSVPRL-PPGRKPPGPPPGPPPPQVLQMYGRKVGFALDLPPRRRDED-MLYSPELAQ
          P...AVSI..LLGH.VP.L.PP.RKPPGPP.GP.P.QVLQMYG.KV.FAL..PP.RRD...MLYSPEL.Q
Retrocopy PPPKAVSIIHLLGHGVPHL>PPDRKPPGPPSGPLPLQVLQMYGCKVDFALCFPPCRRDLH>MLYSPELVQ

Parental  RGHDDDVSSTSEDDGYPEDMDQEKHDDSSDDSDTDRSDGESEGDEFAHRDDNDRDNNEEKKSGLSVRFAD
          RGHD.DV.STSED.GYPE.MDQ.KHDDS...SDTDRSDGES.GDEF.H..D...DNNEE.KSGLSV.FAD
Retrocopy RGHDKDVPSTSEDYGYPEGMDQDKHDDSTNGSDTDRSDGESDGDEFVHCGDSE*DNNEENKSGLSVGFAD

Parental  MPGKSRKKKKNMKEPTPVQAMMLRMAGQEIPEEGREVEEFSEDDDDDDSEDSAAEKQSQKQHKEDSHSDG
          MPGKSRKK.KNMKE..P..AMMLRMAGQ..PEEGREVEEFSEDDD.DDS...AAEKQS.KQ.KEDSHSDG
Retrocopy MPGKSRKKEKNMKELIPLKAMMLRMAGQKLPEEGREVEEFSEDDDEDDS---AAEKQSHKQRKEDSHSDG

Parental  TSASSQQQA-PPQSVPPSQIQAPPMPGPPPLGPPPAPPL-GPGPPT
          TSASS.QQ..PPQSVP.SQ.QAPPMPGPPP..PPPA.PL..PG.PT
Retrocopy TSASSKQQTPPPQSVPSSQTQAPPMPGPPPTDPPPALPLPPPGTPT

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_678 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 22 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014759	1 retrocopy	retro_btau_20,
Canis familiaris	ENSCAFG00000012926	2 retrocopies	retro_cfam_1369, retro_cfam_1911,
Callithrix jacchus	ENSCJAG00000021611	1 retrocopy	retro_cjac_1737,
Homo sapiens	ENSG00000084463	2 retrocopies	retro_hsap_1878, retro_hsap_4719,
Gorilla gorilla	ENSGGOG00000004448	3 retrocopies	retro_ggor_1375, retro_ggor_1711, retro_ggor_2932,
Macropus eugenii	ENSMEUG00000013971	1 retrocopy	retro_meug_1952,
Myotis lucifugus	ENSMLUG00000015216	1 retrocopy	retro_mluc_1074,
Macaca mulatta	ENSMMUG00000019299	1 retrocopy	retro_mmul_1329,
Monodelphis domestica	ENSMODG00000017949	1 retrocopy	retro_mdom_143,
Mustela putorius furo	ENSMPUG00000011619	1 retrocopy	retro_mputfur_280,
Mus musculus	ENSMUSG00000030216	1 retrocopy	retro_mmus_2740,
Nomascus leucogenys	ENSNLEG00000003926	1 retrocopy	retro_nleu_2651,
Oryctolagus cuniculus	ENSOCUG00000017177	1 retrocopy	retro_ocun_974,
Otolemur garnettii	ENSOGAG00000010518	1 retrocopy	retro_ogar_207,
Ochotona princeps	ENSOPRG00000015008	3 retrocopies	retro_opri_107, retro_opri_1159, retro_opri_678 ,
Pongo abelii	ENSPPYG00000004323	3 retrocopies	retro_pabe_1558, retro_pabe_2099, retro_pabe_3663,
Pan troglodytes	ENSPTRG00000004724	3 retrocopies	retro_ptro_1260, retro_ptro_1637, retro_ptro_3136,
Rattus norvegicus	ENSRNOG00000005505	3 retrocopies	retro_rnor_1287, retro_rnor_2726, retro_rnor_741,
Rattus norvegicus	ENSRNOG00000049593	1 retrocopy	retro_rnor_740,
Sorex araneus	ENSSARG00000007085	1 retrocopy	retro_sara_753,
Sarcophilus harrisii	ENSSHAG00000016649	1 retrocopy	retro_shar_81,
Tupaia belangeri	ENSTBEG00000003394	1 retrocopy	retro_tbel_2213,