RetrogeneDB ID: retro_opri_395

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_10731:39711..40821(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAPOLG
• Ensembl ID: ENSOPRG00000009630
• Aliases: None
• Description: poly(A) polymerase gamma [Source:HGNC Symbol;Acc:14982]

Sequence

>retro_opri_395
ATGCCGCCATTTCCAGTTACAACGCAGGGGTCAGAGCAAGTGCCCCAGAACCACTATGGCGTTACTTCTCCTATCAGCCT
AGCAGCCCCCAAGGAGACTGACTGCATCCTCACCCAGAAACTCATCGAGACTCTGAAGCCCTTTGGGGTGTTTGAAGAGG
AAGAGGAACTGCAGCGCAGAATTTTAATTTTGGAAAAATTAAATAACCTGGTTAAAGAGTGGATACATGAAATCAGTGAA
AGTAAGAATCGTCCACAGTCAGTGATTGAAAACGTTGGCGAAAAAATTGTTACATTTGGATCTTACAGATTAGGAGTACA
TACAAAACGTGCTGATATTGATGTGCTGTGTGTTGCACCAAGTCATGTTGATGAAAGTGACTTTTTCACCTCATTCTATG
ACAAGTTGAAATTATAGGAAGAAGTAAAGGATTTAAGAGCTGTTGAAGAGGCATTTGTACCAGTTATCAAACGTTGTTTT
GATGGGATAGAGATTGATATTTTGTTTGTAACATTAGCCCTGCAGACCATTCCCGAAGATTTGGACCTACAAGATGATAG
TCTACTTAAAAACTTAAACCATAAGATGCATAAGAAGTCTTAATGGTTGCAGGGTAACCGATGAAATTTTACATCTAGTA
CCAAACACTGACAACTTCAGGTTAACACTGAGAGCTGTCAAACTGTGGGCCAAACGCCACAACTTCTATTCCAATGTATC
AGGTTTCCTCGGTCGTGTTTCCTGGGCCATGCTGATAGCAAGAACTTGTCAGCTTTATCCAAAGGCAATACCATCAGCTC
TTGTACTTAATTTTTTCTTGGTATTTTCTAAACGGGAATGGCCAAATCCAGAGCTATTGAAACAGCCTGAAGAATGCAAA
TTTAATTTGTCTTTATGGGATCCAAGGGTAAGCCCCAGTGATGGGTACCTTCTTATGCTACATATACACCAGCATACCCA
CAGCAGAACTCCATGTACAATGTGTCCGTTTCAACAAGGATGGTCATGGTTGAGAAGTTTAAACAAGGTCTTGCTATCAC
AGATGGAATTTTGCTGAGTAAGGCAGAGTGGTCCAAACTCTTTGAAGCTCCTAACTTCTTTCACAAGTAC

Alignment

ORF - retro_opri_395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.16 %
• Parental protein coverage: 50.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKEMSANTMLDSQRQQKHYGITSPISLACPKEIDHIYTQKLIDAMKPFGVFEDEEELNHRLVVLGKLNNL
          M......T....Q..Q.HYG.TSPISLA.PKE.D.I.TQKLI...KPFGVFE.EEEL..R...L.KLNNL
Retrocopy MPPFPVTTQGSEQVPQNHYGVTSPISLAAPKETDCILTQKLIETLKPFGVFEEEEELQRRILILEKLNNL

Parental  VKEWISDISESKNLPPSVVATVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVERSDFFQSFFEKLKHQD
          VKEWI..ISESKN.P.SV...VG.KI.TFGSYRLGVHTK.ADID.LCVAP.HV..SDFF.SF..KLK...
Retrocopy VKEWIHEISESKNRPQSVIENVGEKIVTFGSYRLGVHTKRADIDVLCVAPSHVDESDFFTSFYDKLKL*E

Parental  GIRNLRAVEDAFVPVIKFEFDGIEIDLVFARLAIQTISDNLDLRDDSRLRSLD-IRCIRSLNGCRVTDEI
          ....LRAVE.AFVPVIK..FDGIEID..F..LA.QTI...LDL.DDS.L..L..IRCIRSLNGCRVTDEI
Retrocopy EVKDLRAVEEAFVPVIKRCFDGIEIDILFVTLALQTIPEDLDLQDDSLLKNLN>IRCIRSLNGCRVTDEI

Parental  LHLVPNKETFRLTLRAVKLWAKRRGIYSNMLGFLGGVSWAMLVARTCQLYPNAAASTLVHKFFLVFSKWE
          LHLVPN...FRLTLRAVKLWAKR...YSN..GFLG.VSWAML.ARTCQLYP.A..S.LV..FFLVFSK.E
Retrocopy LHLVPNTDNFRLTLRAVKLWAKRHNFYSNVSGFLGRVSWAMLIARTCQLYPKAIPSALVLNFFLVFSKRE

Parental  WPNPVLLKQPEESNLNLPVWDPRVNPSDRYHLMPII-TPAYPQQNSTYNVSTSTRTVMVEEFKQGLAVTD
          WPNP.LLKQPEE...NL..WDPRV.PSD.Y.LM..I.TPAYPQQNS.YNVS.STR.VMVE.FKQGLA.TD
Retrocopy WPNPELLKQPEECKFNLSLWDPRVSPSDGYLLMLHI<TPAYPQQNSMYNVSVSTRMVMVEKFKQGLAITD

Parental  EILQGKSDWSKLLEPPNFFQKY
          .IL..K..WSKL.E.PNFF.KY
Retrocopy GILLSKAEWSKLFEAPNFFHKY

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_395 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 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000014028	4 retrocopies	retro_chof_2125, retro_chof_2361, retro_chof_2456, retro_chof_2571,
Ochotona princeps	ENSOPRG00000009630	4 retrocopies	retro_opri_208, retro_opri_395 , retro_opri_827, retro_opri_861,
Ictidomys tridecemlineatus	ENSSTOG00000010861	1 retrocopy	retro_itri_1616,
Tursiops truncatus	ENSTTRG00000006237	1 retrocopy	retro_ttru_475,