RetrogeneDB ID: retro_tbel_4314

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_7641:21349..22218(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EFCAB14
• Ensembl ID: ENSTBEG00000006829
• Aliases: None
• Description: EF-hand calcium binding domain 14 [Source:HGNC Symbol;Acc:29051]

Sequence

>retro_tbel_4314
TGCTCTAAGATCTGTTTTCCCCTCTGTGCTTTCATCATCCTTGCTGCCTGTATTGTGGCCTGTGTGGGCCTGGGGTGAAT
GCAAATTGCTGTCAAGGAGAATCTGGATGCACTCTAGAAAAAATTCAGAACCGTGAAGTCTAATCAGAAAAGGTCATTGC
AAGAAATCTTTAAACTTAATAAAAACAACTCAGCCAACAAAAACAACTTGAGAAGTTTGAATCTGGAGAATTGGGCTTGA
ACAACGTCTGGATAAACATCACAGAAACAAATAAGCTGATTTCTCTGTTGACTTCTGCCGTAAACCACCTCAAAGTCAAT
GTTAAGTCAGTTGCAGACATAATTAGCCTTCCTATGGCTGTGGAGGGATTTCAGAAGAGGGTCGCTTCCCTTGGTGATAC
GTTAGACAGCGTCCCTCTTGCTGTGGAGGCAATACAGAAAACTCTGGACGGACATAAGGAAACCATGGAGTTACGGCAGA
GTGAAACAAATCAGCCCATCCTGAAGGAGACTAGTGGAAGCAGCCAGATCATTATTCCATCACCTCCAGCTACATTAGAA
CCTGAAAATAAAACCTACAGTGAGAGTTTGAAACAGGATATCCTGTACCTTCATGACACTTTAGAAGAGGTAAACTGTGC
CCTAGTGGGGTACCAGAGACAGAACGATCTCAGATTCAAGGGGATGAATGAGACAGTAATCTTACTCAGAGAGTCAACCT
CATCGAAAGTGATATGGTTGCCATGAACAAGGAAAAAAAGAGAGCAACCTGTCCCTCAGCAGTATGGGTAACAGAGCTGC
CACTCTGAAAAGAGACTCTTTGGATCAAGAGTCCAACAAAGAGATATACTGGAAACCCAAGACATAAAG

Alignment

ORF - retro_tbel_4314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.31 %
• Parental protein coverage: 58.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CCKICYPLCAFVILAACVVACVGLVWMQIALKEDLDALKEKFRTMESNQKSSFQEIPKLNE-ELLSKQKQ
          C.KIC.PLCAF.ILAAC.VACVGL..MQIA.KE.LDAL..KFRT..SNQK.S.QEI.KLN....LS.QKQ
Retrocopy CSKICFPLCAFIILAACIVACVGLG*MQIAVKENLDAL*KKFRTVKSNQKRSLQEIFKLNK<KQLSQQKQ

Parental  LEKIESGELGLNKVWINITEMNKQISLLTSAVNHLKANVKSAADLISLPATVE-LQKSVASIGSTLNSVH
          LEK.ESGELGLN.VWINITE.NK.ISLLTSAVNHLK.NVKS.AD.ISLP..VE..QK.VAS.G.TL.SV.
Retrocopy LEKFESGELGLNNVWINITETNKLISLLTSAVNHLKVNVKSVADIISLPMAVEGFQKRVASLGDTLDSVP

Parental  LAVEAVQKTVDEHKKTLELLQSDMNQHILKETSGSNQIT-PSPPATLDPDNKTHSENLKQDILYLHDSLE
          LAVEA.QKT.D.HK.T.EL.QS..NQ.ILKETSGS.QI..PSPPATL.P.NKT.SE.LKQDILYLHD.LE
Retrocopy LAVEAIQKTLDGHKETMELRQSETNQPILKETSGSSQIIIPSPPATLEPENKTYSESLKQDILYLHDTLE

Parental  EVNSALVGYQRQNDLR-LEGMNETVSNLTQRVNLIESDMVAMSKVEKRA-NLSLSTMGDRPATLKRESLN
          EVN.ALVGYQRQNDLR...G..E..SNLTQRVNLIESDMVAM.K..KRA.NLSLS.MG.R.ATLKR.SL.
Retrocopy EVNCALVGYQRQNDLR<IQG-DE*DSNLTQRVNLIESDMVAMNKEKKRA<NLSLSSMGNRAATLKRDSLD

Parental  PVTNRS-DTLKTQSIK
          ...N...D.L.TQ.IK
Retrocopy QESNKE<DILETQDIK

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_4314 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4314 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000014593	1 retrocopy	retro_mluc_2389,
Macaca mulatta	ENSMMUG00000004866	1 retrocopy	retro_mmul_242,
Ictidomys tridecemlineatus	ENSSTOG00000016250	1 retrocopy	retro_itri_1166,
Tupaia belangeri	ENSTBEG00000006829	1 retrocopy	retro_tbel_4314 ,