RetrogeneDB ID: retro_itri_1616

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393575.1:1061845..1063318(+)
• Located in intron of: ENSSTOG00000000578

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAPOLG
• Ensembl ID: ENSSTOG00000010861
• Aliases: None
• Description: poly(A) polymerase gamma [Source:HGNC Symbol;Acc:14982]

Sequence

>retro_itri_1616
TCCTCGGCGATCAGCCTGGCCGCCCCCAGGGACACGGACCACGAGCTCACGCAGAAGCTGGTGGAGACCCTGAAGCCCTT
CGGGGTGTTCGAGGAGGAAGAGGAGCTGCAGCGCAGGATTCTAATTTTGGAAAAACTAAACAACTTGGTGAAGGAGTGGA
TACGCGAAATCAGTGAAAGCAAGAGTCTTCCGCAAGCTGTGACTGAGAGTGTTGGGGGGAAAATTTTCACGTTCGGCTCT
TACAGACTGGGAGTGCACACGAAGGGTGCCGATATCGATGCGCTGTGCGTCGCGCCGAGACATGTCGACCGCAGCGACTT
TTTCACCTCATTTTATGATAAATTGAAACTACAGGAAGAAGTCAAAGATTTAAGGGCCGTTGAGGAGGCATTTGTACCAG
TGATCAAACTGTGTTTTGATGGGATAGAGATAGATATTTTGTTTGCAAGATTAGCATTGCAGACTATTCCAGAAGATTTG
GACTTAAGAGATGACAGTCTGCTTAAAAATTTAGATATTAGATGCATAAGAAGCCTAAATGGCTGCCGGGTAACTGATGA
AATTTTGCATCTAGTACCAAACATTGACAACTTCAGGCTAACTCTGAGAGCCATCAAATTGTGGGCCAAATGCCACAATA
TCTATTCCAATATATTAGGTTTCCTTGGAGGTGTTTCCTGGGCTATGCTAGTAGCAAGAACCTGCCAGCTTTATCCAAAT
GCAATAGCATCAACTCTTGTTCGTAAATTTTTCCTGGTGTTTTCTGAATGGGAATGGCCAAATCCAGTGTTATTAAAAGA
GCCTGAAGAACGAAATCTTAATTTACCTGTGTGGGACCCAAGAGTAAATCCCAGTGATAGGTACCATCTTATGCCTATAA
TCACACCAGCATATCCACAGCAGAACTCCACATACAATGTTTCAGTTTCAACCAGGATGGTCATGATTGAGGAGTTTAAG
CAAGGGCTTGCTATCACACATGAAATTTTGCTGAACAAGGCAGAGTGGTCCAAACTTTTTGAAGCTCCAAGCTTCTTTCA
AAAGTACAAACATTATATTGTACTTCTGGCAAGTGCACCAACAGAAAAACAACATCTAGAATGGGTGGGCTTGGTGGAAT
CAAAGATCCGAATTCTGGTTGGGAGCTTAGAGAAGAATGAATTTATTACACTGGCACACGTGAATCCCCAGTCATTTCCA
GCACCCAAAGAAAATCCTGACAAGGAAGAATTTCGTACAATGTGGGTGATTGGGTTAGTGTTAAAAAAGCCAGAAAATTC
TGAAACTCTCAGTATCGATCTCACCTATGATATTCAGTCTTTCACAGATACAGTTTATAGGCAAGCAATAAATAGTAAGA
TGTTTGAGATGGATATGAAAATTGCTGCAATGCATTTAAGAAGAAAGGAGCTTCATCAACTACTCCCTAATCATGTTCTT
CAGAAAAAGAAAACACATTCTGCAGAAGGTATA

Alignment

ORF - retro_itri_1616 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.52 %
• Parental protein coverage: 66.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSPISLACPKEIDHIYTQKLIDAMKPFGVFEDEEELNHRLVVLGKLNNLVKEWISDVSESKNLPPSVVAT
          .S.ISLA.P...DH..TQKL....KPFGVFE.EEEL..R...L.KLNNLVKEWI...SESK.LP..V...
Retrocopy SSAISLAAPRDTDHELTQKLVETLKPFGVFEEEEELQRRILILEKLNNLVKEWIREISESKSLPQAVTES

Parental  VGGKIFTFGSYRLGVHTKGADIDALCVAPRHVERSDFFQSFFEKLKHQDGIRNLRAVEDAFVPVIKFEFD
          VGGKIFTFGSYRLGVHTKGADIDALCVAPRHV.RSDFF.SF..KLK.Q.....LRAVE.AFVPVIK..FD
Retrocopy VGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFD

Parental  GIEIDLVFARLAIQTISDNLDLRDDSRLRSLDIRCIRSLNGCRVTDEILHLVPNKETFRLTLRAVKLWAK
          GIEID..FARLA.QTI...LDLRDDS.L..LDIRCIRSLNGCRVTDEILHLVPN...FRLTLRA.KLWAK
Retrocopy GIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAK

Parental  RRGIYSNMLGFLGGVSWAMLVARTCQLYPNAAASTLVHKFFLVFSKWEWPNPVLLKQPEESNLNLPVWDP
          ...IYSN.LGFLGGVSWAMLVARTCQLYPNA.ASTLV.KFFLVFS.WEWPNPVLLK.PEE.NLNLPVWDP
Retrocopy CHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVRKFFLVFSEWEWPNPVLLKEPEERNLNLPVWDP

Parental  RVNPSDRYHLMPIITPAYPQQNSTYNVSTSTRTVMVEEFKQGLAVTDEILQGKSDWSKLLEPPNFFQKYR
          RVNPSDRYHLMPIITPAYPQQNSTYNVS.STR.VM.EEFKQGLA.T.EIL..K..WSKL.E.P.FFQKY.
Retrocopy RVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMIEEFKQGLAITHEILLNKAEWSKLFEAPSFFQKYK

Parental  HYIVLTASASTEENHLEWVGLVESKIRVLVGNLERNEFITLAHVNPQSFPGNKEHHKDNNYVSMWFLGII
          HYIVL.ASA.TE..HLEWVGLVESKIR.LVG.LE.NEFITLAHVNPQSFP..KE.........MW..G..
Retrocopy HYIVLLASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEEFRTMWVIGLV

Parental  FRRVENAESVNIDLTYDIQSFTDTVYRQANNINMLKEGMKIEATHVKKKQLHHYLPAEILQKKKKQSLSD
          ....EN.E...IDLTYDIQSFTDTVYRQA.N..M....MKI.A.H...K.LH..LP...LQKKK..S...
Retrocopy LKKPENSETLSIDLTYDIQSFTDTVYRQAINSKMFEMDMKIAAMHLRRKELHQLLPNHVLQKKKTHSAEG

Parental  V
          .
Retrocopy I

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1616 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1616 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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,