RetrogeneDB ID: retro_opri_444

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_12273:165..803(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB4
• Ensembl ID: ENSOPRG00000016650
• Aliases: None
• Description: MOB family member 4, phocein [Source:HGNC Symbol;Acc:17261]

Sequence

>retro_opri_444
GCAGTGTTGAGGTAGAACAGGCAGAGAATCAAGACACAGGATTTCTGGAACTGGCCTGATGAATCCTTTTATGAGATTGG
CAGTATCTTGCTGTTTGGCAGTGTATTCAACAGCACATAAGGACAACTTGCCCCAATAACTGATAAAACTTTTGAACTAC
CTGAATGTCAAGATGAAGACATGTGGAAGTATGAATATTTCAGGAAATTCTGTCTTGAGCTAAATGGATTTACTGTCAAA
CATCAGAGTGAATGTTCTCCAGATGGTTGCACTGAAATAACAGCAACTAAGCAATAGATTTTTCAGTGTACAGCTCATAA
AACTCCCAAATAGTGTCTGCTACAGACTGTACTAGACACACGCTTGATGGTACTGCATATCTTCTAAAAAGCAATAAATA
TTTCTCTTGCAGGGTTAGCATAAAGGAATCATCAACAGCAAAACTGGAATCAGTACGCCGCAGGGTTTGCAGAGTTTTTT
CACATGCTCATTTTCACCACCAGCAGATAGTTAATCAAAATTAAAATGAAAAAATTTTGTTATTTTTTACTAAATTTGTA
ATGAAATACAATTTGAATCTCAAGGACAAACTACCAGTTTTAGAAGAAGTTCAGGATTTAGTTTCTGATGAAAGTGAA

Alignment

ORF - retro_opri_444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.16 %
• Parental protein coverage: 96.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AVLRRNRPGTKAQXXXXXXXXXFDEMDSTL-AVQQYIQQNIRADCSN-IDKILEPPEGQDEGVWKYEHLX
          AVLR.NR...K.Q.........F.E..S.L.AV.Q.IQQ.IR..C.N..DK..E.PE.QDE..WKYE...
Retrocopy AVLR*NRQRIKTQDFWNWPDESFYEIGSIL<AVWQCIQQHIRTTCPN>TDKTFELPECQDEDMWKYEYFR

Parental  XXXXXXXXXXXXXXSECHPDTCTQMTATEQWIFLCAAHKTPKEC-PAIDYTRHTLDGAACLLNSNKYFPS
          ..............SEC.PD.CT..TAT.Q.IF.C.AHKTPK.C..A.D.TRHTLDG.A.LL.SNKYF..
Retrocopy KFCLELNGFTVKHQSECSPDGCTEITATKQ*IFQCTAHKTPK*C<SATDCTRHTLDGTAYLLKSNKYFSC

Parental  RVSIKESSVAKLGSVCRRIYRIFSHAYFHHRQIFDEYENETFLCHRTKFVMKYNLMSKDNLIVPILEEEV
          RVSIKESS.AKL.SV.RR..R.FSHA.FHH.QI.....NE..L...TKFVMKYNL..KD.L..P.L.EEV
Retrocopy RVSIKESSTAKLESVRRRVCRVFSHAHFHHQQIVNQN*NEKILLFFTKFVMKYNLNLKDKL--PVL-EEV

Parental  QNSVSGESE
          Q..VS.ESE
Retrocopy QDLVSDESE

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_444 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 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004020	2 retrocopies	retro_cjac_1960, retro_cjac_3238,
Cavia porcellus	ENSCPOG00000012746	2 retrocopies	retro_cpor_318, retro_cpor_804,
Homo sapiens	ENSG00000115540	2 retrocopies	retro_hsap_2275, retro_hsap_906,
Gorilla gorilla	ENSGGOG00000009005	2 retrocopies	retro_ggor_733, retro_ggor_743,
Latimeria chalumnae	ENSLACG00000015430	1 retrocopy	retro_lcha_112,
Macaca mulatta	ENSMMUG00000016547	1 retrocopy	retro_mmul_829,
Monodelphis domestica	ENSMODG00000012305	2 retrocopies	retro_mdom_1333, retro_mdom_963,
Oryctolagus cuniculus	ENSOCUG00000005712	1 retrocopy	retro_ocun_30,
Otolemur garnettii	ENSOGAG00000000272	1 retrocopy	retro_ogar_2739,
Ochotona princeps	ENSOPRG00000016650	2 retrocopies	retro_opri_444 , retro_opri_812,
Pongo abelii	ENSPPYG00000013047	6 retrocopies	retro_pabe_1943, retro_pabe_2021, retro_pabe_3600, retro_pabe_781, retro_pabe_795, retro_pabe_970,
Sarcophilus harrisii	ENSSHAG00000017821	1 retrocopy	retro_shar_351,
Ictidomys tridecemlineatus	ENSSTOG00000021024	1 retrocopy	retro_itri_727,
Tarsius syrichta	ENSTSYG00000001726	1 retrocopy	retro_tsyr_1673,