RetrogeneDB ID: retro_itri_1056

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393365.1:471004..471944(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WNT8A
• Ensembl ID: ENSSTOG00000007249
• Aliases: None
• Description: wingless-type MMTV integration site family, member 8A [Source:HGNC Symbol;Acc:12788]

Sequence

>retro_itri_1056
CATCTCACCCCTACTACCAATGTGGGCTTGAGTACCCAGAGTGGCATTGAGCAGTATAAGTTCCTTTTTTTTTGTTATCA
TTGGAACTGCCCTGAAAACACTCTCCAGCTCACCACCCACAACAGGCTGAGAAATGCCAACAGAGAGATTTCCTTCATTC
ATGCCATCAGCTCTGCCTGAGTCATGTACACCATCACTAAATACTGTAGCATGGGTGACTTTGAAAACTGTGACTGTGAT
GAGTCAAAAACAGAAAAACAGGAGGCCATAACTGGATCTAGCGAGGCTGCAGCGACAATGTGGAATTTGGGGAAAGGATC
TCCAAACTATTTGTGAACAATCTGGAGAAGGGGAAGGATGCCAAAGCCCTGATGAGTCTTCACAACAGGGCCGGCTGGCA
GGCAGTAAGAGTCACCGTGGAAAGAATCTGCAAATGCCATAATATCTCAGAGAGCTGCAGCATCCAGACATGCTGGCTGC
AGCTGGCTCACTGCTGGGAGATGGGAGACTACCTAAAGGACAAGCATGACCAGTCACTGAAAATTGAGAAGGATAAGCAG
CAGCTAAGGGCTGGGAACAACGCCGAGGGTTGCTGAGCTCCCACTGAGGCTCTTCCTCCTAGCATAGAAGCTAAGATAAT
CATTTTAGAGAAATCTCCAGACTACATACCTGCAGTTCCAGCCTGGGCATTTATGACACAAAGGGTCGAAAGTGCCTGCA
GACCAGCTGCAATACATTCAAGTAGGAGCTTGAACACAGCTGTGGGCACCTGTGCACTGAGTGTGAGCTACAGGTGGAAG
AGAGGAAGACTGAAGCCAAGAACAGCTGTAACAGCAAATTTCAATGGGGCTGCATGATCAAGTACCACCAGCTTAGGCAT
GTGGTGAACAAGTACTACTGCATGCACTCCCCAGACAGTGCCCAGGCCTGATGCAACAGG

Alignment

ORF - retro_itri_1056 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.56 %
• Parental protein coverage: 89.71 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YLTYTTSVALGAQSGIEECKFQFAWERWNCPENALQLSTHNRLRSATRETSFIHAISSAGVMYTITKNCS
          .LT.TT.V.L..QSGIE..KF......WNCPEN.LQL.THNRLR.A.RE.SFIHAISSA.VMYTITK.CS
Retrocopy HLTPTTNVGLSTQSGIEQYKFXXXXYHWNCPENTLQLTTHNRLRNANREISFIHAISSA*VMYTITKYCS

Parental  MGDFENCGCDESK-NGKTGGHGWIWGGCSDNVEFGERISKLFVDSLEKGKDARALMNLHNNRAGRLAVRA
          MGDFENC.CDESK.N.KTGGH.WI..GCSDNVEFGERISKLFV..LEKGKDA.ALM.LHN.RAG..AVR.
Retrocopy MGDFENCDCDESK<NRKTGGHNWI*RGCSDNVEFGERISKLFVNNLEKGKDAKALMSLHN-RAGWQAVRV

Parental  TMKRICKCHGISGSCSIQTCWLQLADFREMGNYLKAKYDQALKIEMDKRQLRAGNSAEGCWAPTEAFLPS
          T..RICKCH.IS.SCSIQTCWLQLA...EMG.YLK.K.DQ.LKIE.DK.QLRAGN.AEGC.APTEA..PS
Retrocopy TVERICKCHNISESCSIQTCWLQLAHCWEMGDYLKDKHDQSLKIEKDKQQLRAGNNAEGC*APTEALPPS

Parental  IEAELIFLEESPDYC-TRNSSLGIYGTEGRECLQNSHNTSKRE-QRSCGHLCTECGLQVEERRTEAVSSC
          IEA..I.LE.SPDY..T..SSLGIY.T.GR.CLQ.S.NT.K.E...SCGHLCTEC.LQVEER.TEA..SC
Retrocopy IEAKIIILEKSPDYI<TCSSSLGIYDTKGRKCLQTSCNTFK*ELEHSCGHLCTECELQVEERKTEAKNSC

Parental  NCKFQWCCTVKCDQCRHVVNKYYCMRSPGSARGRGNR
          N.KFQW.C..K..Q.RHVVNKYYCM.SP.SA....NR
Retrocopy NSKFQWGCMIKYHQLRHVVNKYYCMHSPDSAQA*CNR

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_1056 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1056 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000007249	1 retrocopy	retro_itri_1056 ,