RetrogeneDB ID: retro_tbel_814

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3074:266252..266918(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ECI2
• Ensembl ID: ENSTBEG00000015862
• Aliases: None
• Description: enoyl-CoA delta isomerase 2 [Source:HGNC Symbol;Acc:14601]

Sequence

>retro_tbel_814
TATGAAGAAATTATGCTTGCACTTAAAGCTGCAAGCAAGGTTGACTTCGTCGTAACTGTTTTAACAGGGAACGGTGACTA
TTACAGTAGTGGGAAAGACCTAACTTCACCGATATTCCACCTGGGGGAGTAGAGGAAAAAGCTAAAAATAGTGGCATTTT
GCTGAGGGATTTTGTACGCTGTTTTATAGATTTCCCTAAGCCTCTGGTTGCAGTGGTAAATGGTCTGGCTGTGGGAATTT
CCGTCACCCTTCTTGGGCTGTTTGATGCTGTGTATGCATCCGACAGGGCAACGTTCCATACCCCATTCAGTACGCTAGGC
CAATGTCCAGAAGGCTGTTTTTCCTACATGTCTCCAAAGATTACGGGCTCAGCCAAGGCAACTGAGATGCTTGTTTTGGG
GAAGAAGTTAACAGCAGGGGAGGCCTGTGTTCAAGGACTTGTTACTGAAGTCTTTCCTGATAGCACGTTTCAGAGAGAAA
GCATATATGCTGAAAGCATTTGCAAAGCTCCCTCCAAATGCCCTGAAAATTTCAAAAGAGGTCATCAGAAACAGGGAGAA
AGAAAAGCTTCACGCTGTTAATGCTGAAGAATGCATCACCCTCCAGGAAAGATGGCTGTCTGAGGAATGCACAAATGGAA
TCATGAACTTCTTATCCAGAAAAGCA

Alignment

ORF - retro_tbel_814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.45 %
• Parental protein coverage: 57.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YEEIMLALKAASEDKSALTVLTGNGDYYCSGN-DLTNFTDIPPGGVEEKAKSSHILLRNFVQCFIDFPKP
          YEEIMLALKAAS......TVLTGNGD.Y.S......NFTDIPPGGVEEKAK.S.ILLR.FV.CFIDFPKP
Retrocopy YEEIMLALKAASKVDFVVTVLTGNGD-YYSSG<ERPNFTDIPPGGVEEKAKNSGILLRDFVRCFIDFPKP

Parental  LIAVVNGPAVGISVTLLGLFDAVYASDRATFHTPFSALGQSPEGCSSYTFPKIMGSAKATEMLVFGKKLT
          L.AVVNG.AVGISVTLLGLFDAVYASDRATFHTPFS.LGQ.PEGC.SY..PKI.GSAKATEMLV.GKKLT
Retrocopy LVAVVNGLAVGISVTLLGLFDAVYASDRATFHTPFSTLGQCPEGCFSYMSPKITGSAKATEMLVLGKKLT

Parental  AGEACAQG-LVTEVFPDSTFQREVWTRLKAYAKLPANTLRVSKNIIRSREREKLRAVNAEECITLEGRWQ
          AGEAC.QG.L....F....F.......LKA.AKLP.N.L..SK..IR.RE.EKL.AVNAEECITL..RW.
Retrocopy AGEACVQG>LLLKSFLIARFREKAYM-LKAFAKLPPNALKISKEVIRNREKEKLHAVNAEECITLQERWL

Parental  SEDCMNAIMNFLSRKA
          SE.C.N.IMNFLSRKA
Retrocopy SEECTNGIMNFLSRKA

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_814 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_814 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009409	1 retrocopy	retro_cfam_536,
Choloepus hoffmanni	ENSCHOG00000009239	1 retrocopy	retro_chof_25,
Procavia capensis	ENSPCAG00000008568	1 retrocopy	retro_pcap_71,
Rattus norvegicus	ENSRNOG00000016369	1 retrocopy	retro_rnor_1179,
Tupaia belangeri	ENSTBEG00000000034	5 retrocopies	retro_tbel_1040, retro_tbel_3676, retro_tbel_4160, retro_tbel_4448, retro_tbel_4710,
Tupaia belangeri	ENSTBEG00000008062	1 retrocopy	retro_tbel_4165,
Tupaia belangeri	ENSTBEG00000015862	2 retrocopies	retro_tbel_2398, retro_tbel_814 ,