RetrogeneDB ID: retro_opri_891

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_4143:30712..32092(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDM2
• Ensembl ID: ENSOPRG00000009677
• Aliases: None
• Description: MDM2 oncogene, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:6973]

Sequence

>retro_opri_891
CCATTGCTTTTGAATTGTTAAAGTCTGTTGGTGCACAAAAAGACACTTACACCATGAAAGAGGTTATATTTTATCTTGGC
CAGTACATTATGACTAAACAATTATATGATGAGAAGCAACAACACATTGTATATTGTTCAAATGATCTTCTTGGCGATTT
GTTTGGAGTTCCAGGCTTCTCTGTGAAAGAGCACAGGAAAATATATACAATAATCTACAGAAACTTGGTAGTAGTCAATC
AGCAGGAACCTTCCGATTCAGGCATGTCTATAAGTGAGGACAGATATCACCCTGAAGGTGGGAATGATGAAAAGGAGCCT
GGTCAAGTGCTGCAGGAAGAGAAGCCTTCATCTTCAAGTTTGGTTTCGAGACCATCTACCTCATCTAGAAGGAGAGCAAT
TAGTGAGACAGAAGAAAATTTGGATGAATTACCTGGTGAACGACAAAGAAGACGCCACAAATCTGATAACATTTCCCTCT
CCTTTGACGAAAGCCTGGCTCTGTGTGTAATACGGGAGCTATGTTGTGAAAGAAGCAGTAGCAGTGAGTCAACAGAGACA
CCGTCAAATTTGGATCTTGATGACCGTGTAAGTGAACACTCAGGTGATTGGCTGGATCAGGATTCATATTCAGATCAGTT
TAGTGTGGAATTTGAAGTTGAATCTCTCGATTCAGAAGATTATAGCCTTAGTGAAGAAGGGCAGGACCTGTCAGATGAAG
AAGATGAGGTTTATCGAGTTCCTCTGTACCAAGCAGGGGAGAGTGACACAGATTCATTTGAAGAAGACCCTGAAATCTCC
CTAGCTGACTACTGGAAGTGTACTTCTTGCCATGAGATGAATCCTCCGCTCCCATCGCATTGCAACAGATGTTGGGCTCT
TCGTGAGAACTGGCTTCCTAGAAGATAAGGGGAAGGATAAAGAGGGAATCTCTAAGAAAGCCCCACTGGAAAACCCGACC
CACTCGGAACAAGACTTTGATGTTCCTGATTGTAAAAAGTCCATAGCAGATGATTCTAAAGAGGCAGGCGTTGAGGAAAA
TGACGATAAAAGCACACAAGCTTCTCAGTCACAAGAGAGCGAGGACTTTTCTCAGCCCTGGACTTCTAACAGCGTTATTT
ATGGCAGCCAAGAGGACGTGAAGGAGTTTGAAAGGGAAGAAACGCAGGAAAAAGAAGAGAGTACGGAACCCAGTTTCCCC
CTGAATGCCATTGAACCGTGTGTGATTTGCCAGGGCCGACCTAAAAATGGTTGCATAGTTCATGGCAAAACCGGACACCT
GATGTCCTGCTTCACTTGTGCCAAGAAGCTGAAGAAAAGGAACAAGCCCTGCCCTGTATGTAGACAGCCTATTCAGATGA
TTGTGCTAACTTATTTCAAC

Alignment

ORF - retro_opri_891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.29 %
• Parental protein coverage: 92.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PLLL-KLLKSVGAQKDTYTMKEVIFYLGQYIMTKRLYDEK--HIVYCSNDL-GDLFGVPSFSVKEHRKIY
          PLLL..LLKSVGAQKDTYTMKEVIFYLGQYIMTK.LYDEK..HIVYCSNDL.GDLFGVP.FSVKEHRKIY
Retrocopy PLLL<ELLKSVGAQKDTYTMKEVIFYLGQYIMTKQLYDEKQQHIVYCSNDLLGDLFGVPGFSVKEHRKIY

Parental  TMIYRNLVVVNQQEPSDSGMSISEDRYHPEGGNDEKEPGQELQEEKPSSSSLVSRPSTSSRRRAISETEG
          T.IYRNLVVVNQQEPSDSGMSISEDRYHPEGGNDEKEPGQ.LQEEKPSSSSLVSRPSTSSRRRAISETE.
Retrocopy TIIYRNLVVVNQQEPSDSGMSISEDRYHPEGGNDEKEPGQVLQEEKPSSSSLVSRPSTSSRRRAISETEE

Parental  NYGELPGERQRRRHKSDNMSLSLDENLAVRLLRKLLYERSSSSEPTDPPSNVDLDDRVSEHSGDWLDQDS
          N..ELPGERQRRRHKSDN.SLS.DE.LA....R.L..ERSSSSE.T..PSN.DLDDRVSEHSGDWLDQDS
Retrocopy NLDELPGERQRRRHKSDNISLSFDESLALCVIRELCCERSSSSESTETPSNLDLDDRVSEHSGDWLDQDS

Parental  DSDQFSVEFEVESLDSEDYSLSEEGQDLSDEDDEVYRVTVYQAGESDTDSFEEDPEISLADYWKCTSCHE
          .SDQFSVEFEVESLDSEDYSLSEEGQDLSDE.DEVYRV..YQAGESDTDSFEEDPEISLADYWKCTSCHE
Retrocopy YSDQFSVEFEVESLDSEDYSLSEEGQDLSDEEDEVYRVPLYQAGESDTDSFEEDPEISLADYWKCTSCHE

Parental  MNPPLPSHCNRCWALRENWLP-EDKGKDKEGISKKAPLENPTHSEQDFDVPDCKKSIADDSKEAGVEEND
          MNPPLPSHCNRCWALRENWLP.EDKGKDKEGISKKAPLENPTHSEQDFDVPDCKKSIADDSKEAGVEEND
Retrocopy MNPPLPSHCNRCWALRENWLP>EDKGKDKEGISKKAPLENPTHSEQDFDVPDCKKSIADDSKEAGVEEND

Parental  DKSTQASQSQESEDFSQPWTSNSVIYGSQEDVKEFEREETQEKEESTEPSFPLNAIEPCVICQGRPKNGC
          DKSTQASQSQESEDFSQPWTSNSVIYGSQEDVKEFEREETQEKEESTEPSFPLNAIEPCVICQGRPKNGC
Retrocopy DKSTQASQSQESEDFSQPWTSNSVIYGSQEDVKEFEREETQEKEESTEPSFPLNAIEPCVICQGRPKNGC

Parental  IVHGKTGHLMSCFTCAKKLKKRNKPCPVCRQPIQMIVLTYFN
          IVHGKTGHLMSCFTCAKKLKKRNKPCPVCRQPIQMIVLTYFN
Retrocopy IVHGKTGHLMSCFTCAKKLKKRNKPCPVCRQPIQMIVLTYFN

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_891 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000005885	1 retrocopy	retro_lafr_715,
Otolemur garnettii	ENSOGAG00000034779	2 retrocopies	retro_ogar_1210, retro_ogar_49,
Ochotona princeps	ENSOPRG00000009677	1 retrocopy	retro_opri_891 ,
Ictidomys tridecemlineatus	ENSSTOG00000014702	1 retrocopy	retro_itri_1731,
Tupaia belangeri	ENSTBEG00000013758	2 retrocopies	retro_tbel_3216, retro_tbel_915,
Tarsius syrichta	ENSTSYG00000002908	2 retrocopies	retro_tsyr_1343, retro_tsyr_984,