RetrogeneDB ID: retro_tbel_4556

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_90068:0..821(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EHD3
• Ensembl ID: ENSTBEG00000010371
• Aliases: None
• Description: EH-domain containing 3 [Source:HGNC Symbol;Acc:3244]

Sequence

>retro_tbel_4556
CTGCCCATCCCTGATAACCACAAGCTCTTCTAGCCTGAGGACCAGGACCTCTTTCCATGTAAGCAGTCTCTGTCCAGAAA
TGCTGTCTTAAGGAAGCTCAATGACCTCATCAGGCGGACACACCAGCCCAGGTCCATCTCTGCATCAACTCTCTCAAGAA
GAAGATGCCCAATATCTCTGTTAAATAGAACAGAAAGAAAGAGCTTGTGAACAACCTGGGAGAGATCTACCAGAAGATTA
AGTGGGAACATCAGATCTGCCCTGGTGACTTCCCAAGCCTGCACACAATGCAGGAACTCGTGCAAACCCAGGACTTTAGC
AAGTCCCAGGCCTTGAAGCTCAAGCTGCTGGACACAGTAGACAACATACTTGCCAGCGACGTTGCCCGGCTGATGGTGAT
GGTGTACCAGGAGGAGTCCCTGATTCCCTCCCAGGCTATGAAAGGCAGTGCCTTCTATGGCACCATGAATGGGTCCCTTG
GGTACAACTGCAGTGAGGGGGCCTATGAGGGAATTGATGATGTTGAGTGGGTGTTAGGCAAGGATAAGCCCAGCTATTAC
AAGATCTATGTGCCATCACCTATTAACAGCAAGATCACAGGTGCCAACGCCAGGAAAGAAGATGGTGAAACCCATGCTGC
CCGACACATTGCCATGGAAGATCTGGAAGCTGACAGACATGATCAAGGACAGGCTGCTGGACCACCAAGAGGTTGCCCTA
GTCAACCACCTCATCAAGGTCAAACGGAGGGGCCAGAAGCTGCCCATTGACCTGCCCCCAACTGATCTCACCCTTCAAAG
GGAGACATGAGTGATGGCCTC

Alignment

ORF - retro_tbel_4556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.35 %
• Parental protein coverage: 50.64 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LLIPDNRKLFEAEEQDLFRDIQSLPRNAALRKLNDLIKRARL-AKVHAYIISSLKKEMPSVFGKDNKKKE
          L.IPDN.KLF..E.QDLF...QSL.RNA.LRKLNDLI.R....A.VH...I.SLKK.MP....K.N.KKE
Retrocopy LPIPDNHKLF*PEDQDLFPCKQSLSRNAVLRKLNDLIRRTHQ<AQVHL-CINSLKKKMPNISVK*NRKKE

Parental  LVNNLAEIYGRIEREHQISPGDFPNLKRMQDQLQAQDFGKFQPLKSKLLEVVDDMLAHDIAQLMVLVRQE
          LVNNL.EIY..I..EHQI.PGDFP.L..MQ...Q.QDF.K.Q.LK.KLL..VD..LA.D.A.LMV.V.QE
Retrocopy LVNNLGEIYQKIKWEHQICPGDFPSLHTMQELVQTQDFSKSQALKLKLLDTVDNILASDVARLMVMVYQE

Parental  ETQRPIQMVKGGAFEGTLHGPFGHGYGEGAGEGIDDAEWVVARDKPMYDEIFYTLSPVDGKITGANAKKE
          E...P.Q..KG.AF.GT..G..G....EGA.EGIDD.EWV...DKP.Y..I.Y..SP...KITGANA.KE
Retrocopy ESLIPSQAMKGSAFYGTMNGSLGYNCSEGAYEGIDDVEWVLGKDKPSYYKI-YVPSPINSKITGANARKE

Parental  -MVRSKLPNSVLGKIWKLADIDKDGMLDDEEFALANHLIKVKLEGHELPNELP-AHLPHPRGRLPSDGV
          .MV...LP.....KIWKL.D..KD..LD..E.AL.NHLIKVK..G..LP..LP.....HP.....SDG.
Retrocopy >MVKPMLPDTLPWKIWKLTDMIKDRLLDHQEVALVNHLIKVKRRGQKLPIDLP<PN*SHPSKGDMSDGL

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_4556 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4556 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
Equus caballus	ENSECAG00000015195	1 retrocopy	retro_ecab_581,
Monodelphis domestica	ENSMODG00000015505	1 retrocopy	retro_mdom_915,
Sarcophilus harrisii	ENSSHAG00000013011	1 retrocopy	retro_shar_114,
Tupaia belangeri	ENSTBEG00000010371	1 retrocopy	retro_tbel_4556 ,