RetrogeneDB ID: retro_opri_208

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3629:56943..58554(-)
• Located in intron of: ENSOPRG00000015994

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_208
AAGCGCTACGGCATCTCCTCGCCCATCAGCCTGGCCACCCCCAAGGAGACGGACTGCGCGCTCACCCAGAAGCTCATCGA
GACCCTGCGGCCCTTCGGCGTGTTCGAGGAGGAGGAGGAGCTGCAGGGCCGGAGCCTGATCCTGGAGAAGTTGAACAAGT
TGGTGAAGGAGTGGATCCGCGAAGTCAGTGCGAGCAAGAGCCTGCCCGAGGTGCTGGTGGAGAGCGTGGGCGGCCGGCTC
TTCACCTTCGGCTCCTACCGCCTGGGCGTGCACACCAAGGGCGCCGACATCGACGCGCTGTGCGTGGCGCCCAGGCACGT
GGACCGCAGCGACTTCTTCACCTCCTTCTACGACAAGCTGAAGCTGCAGGAGGAGGTGAAGGACCTGCGGGCCGTGGAGG
AGGCGTTCGTGCCGGTCATAAAGCTGTGTTTTGATGGGGTAGAGATCGACATTTTGTTTGCAAGGTTGGCGCTGCAGACC
ATTCCAGAAGACTTGGATTTGAGGGATGACAGTTTGCTCAAGAACTTAGATATCAGATGCATCAGGAGTCTTAACGGTTG
CCGGGTAACCGATGAGATATTACACCTGGTCCCAGACATGGACAACTTCAGGTTAACGCTGAGAGCTATCAAGCTGTGGG
CCAAGTGCCACAATATCTACTCCAACATACTCGGCTTCCTGGGCGGCGTTTCCTGGGCCATGCTGGTGGCGAGAACCTGC
CAGCTCTACCCGAATGCGGTAGCCTCCACTCTGGTGCGTAAATTTTTCTTGGTGTTTTCGGAATGGGAGTGGCCCAACCC
GGTGCTGCTCAAAGAGCCGGAGGAGCGGAACCTGAACCTGCCGGTCTGGGACCCGAGAGTGAACCCCAGTGACCGCTACC
ACCTGATGCCGATCATCACCCCGGCATACCCGCAGCAGAACTCCACCTACAACGTGTCCGTCTCCACCAGGAGGGTCATG
GTGGAGGAGTTTAAACAAGGCCTCGCCATCACACACGAGATCCTGCTCAACAAGGCAGAGTGGTCTAAACTTTTTGAAGC
TCCAAGCTTCTTCCAGAAGTACAAGCACTACATCGTTCTTATAGCAAGTGCGCCGACGGAGAAGCAGCATCTGGAGTGGG
TCGGCCTGGTGGAGTCCAAGATCCGGATCCTAGTCGGGAGCCTGGAGAAGAATGAGTTCATCACCCTGGCGCACGTGAAC
CCCCAGTCGTACCCGGCACCCAAAGAGAAGCCCAAGCAGGAGGAGTTCTGCACCATGTGGGTGATCGGGCTGGTGCTGAA
GAGGCCCGAGAACTCCGAGGTGCTCAGCGTGGACCTCACCTACGACATCCAGTCGTTCACTGACACCGTGTATCGGCAGG
CCATCAACAGCAAGATGTTTGAGATGGATATGAAAGTTGCTGCCATGCATTTGAGAAAGAAAGAGCTCCAGGAGCTGCTC
CCGAACCACGTATTTCAGAAAAAGAAGACCCACCCGGCAGAGGGCGTCACCCTGACAGCCACGAGTGATGATGGCAGTGT
CGGGACAGACAGCGAAGACAGCGTGTCCACACCCTTGCCCCCTGGCCTCTTGACTGGCAGCTCCCAGGACACCAGCAGCC
CCGCCCCACCC

Alignment

ORF - retro_opri_208 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.77 %
• Parental protein coverage: 72.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KHYGITSPISLACPKEIDHIYTQKLIDAMKPFGVFEDEEELNHRLVVLGKLNNLVKEWISDISESKNLPP
          K.YGI.SPISLA.PKE.D...TQKLI....PFGVFE.EEEL..R...L.KLN.LVKEWI...S.SK.LP.
Retrocopy KRYGISSPISLATPKETDCALTQKLIETLRPFGVFEEEEELQGRSLILEKLNKLVKEWIREVSASKSLPE

Parental  SVVATVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVERSDFFQSFFEKLKHQDGIRNLRAVEDAFVPVI
          ..V..VGG..FTFGSYRLGVHTKGADIDALCVAPRHV.RSDFF.SF..KLK.Q.....LRAVE.AFVPVI
Retrocopy VLVESVGGRLFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVI

Parental  KFEFDGIEIDLVFARLAIQTISDNLDLRDDSRLRSLDIRCIRSLNGCRVTDEILHLVPNKETFRLTLRAV
          K..FDG.EID..FARLA.QTI...LDLRDDS.L..LDIRCIRSLNGCRVTDEILHLVP....FRLTLRA.
Retrocopy KLCFDGVEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVPDMDNFRLTLRAI

Parental  KLWAKRRGIYSNMLGFLGGVSWAMLVARTCQLYPNAAASTLVHKFFLVFSKWEWPNPVLLKQPEESNLNL
          KLWAK...IYSN.LGFLGGVSWAMLVARTCQLYPNA.ASTLV.KFFLVFS.WEWPNPVLLK.PEE.NLNL
Retrocopy KLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAVASTLVRKFFLVFSEWEWPNPVLLKEPEERNLNL

Parental  PVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSTSTRTVMVEEFKQGLAVTDEILQGKSDWSKLLEPPNF
          PVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVS.STR.VMVEEFKQGLA.T.EIL..K..WSKL.E.P.F
Retrocopy PVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRRVMVEEFKQGLAITHEILLNKAEWSKLFEAPSF

Parental  FQKYRHYIVLTASASTEEHHLEWVGLVESKIRVLVGNLERNEFITLAHVNPQSFPGNKEHHKDNNYVSMW
          FQKY.HYIVL.ASA.TE..HLEWVGLVESKIR.LVG.LE.NEFITLAHVNPQS.P..KE..K......MW
Retrocopy FQKYKHYIVLIASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSYPAPKEKPKQEEFCTMW

Parental  FLGIIFRRVENAESVNIDLTYDIQSFTDTVYRQA-NNIMLKEGMK-EATHVKKKQLHHYLPAEILQKKKK
          ..G....R.EN.E....DLTYDIQSFTDTVYRQA.N..M....MK..A.H..KK.L...LP....QKKK.
Retrocopy VIGLVLKRPENSEVLSVDLTYDIQSFTDTVYRQAINSKMFEMDMKVAAMHLRKKELQELLPNHVFQKKKT

Parental  QSLSDVSRSGLQSKRSSLDSNCLDS-SRDTDNGTPFNSPVSTDKPSKP
          .....V......S...S......DS.S.....G....S...T..P..P
Retrocopy HPAEGVTLTA-TSDDGSVGTDSEDSVSTPLPPGLLTGSSQDTSSPAPP

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_208 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,