RetrogeneDB ID: retro_tbel_2398

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_109978:3792..4663(-)
• 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_2398
ACTCTTGGCAACCTGCCCAAGGACAGTGCCAGGCAGAACGACCTGGATTTAGTGTCCAGTTTTGAGTTCTTCTCCTGAAT
CCTTCAGCCAGGTGCAGCCTGGAGCTGACAGGAAACTAGCTGAGTATCAAACGACCTCCGAAGATGGCATAACAAAGATC
ATGTTCAACCGGCCCACCAAAAAGAATGCTGCCAGCACCCAGATGTATGAAGAAATTAAACTTGCACTTAAAGCTGCAAG
CAAGGACGACTCCATCATAACTGTTTTAACAGGGAACGGTGACTATTACAGGAGTGGGGATGACCTAACTTCACCAATAG
TCCACCTGGGGGAGTAGAGGAAAGAGCTTAAAATAGTGGCATTTTGCTGAGGGATTTTGTACTCTGTTTTATAGATTTCC
CTAAGCCTCTGATTGCAGTGGTAAACTGTCCAGCTGTGGGAACTTCCGTCACCCTTCTAAGGCTGTTTGATGTTGTGTAC
GCATCTGACAGGGCAATGTTGCATACCCCATTCAGTACACTAGGCCAAAGTCCAGAAGGATGTTCCTCCTACGTATTTCC
AAAGATAATGGGCTCAGCCAAGGCAACTGAGATGCTTGTTTTGGGGAAGAAGTTAACAGCAGGGGAGGCATGGGCTCAAG
GACTTGTTACTGAAGTCTTTCCTGATAGCACGTTTCAGAGAGAAAGCATATATGCTGAAAGCATTTGCAAAGCTCCCTCC
AAATGCCCTGAAAATTTCAAAAGAGGTCATCAGAAACAGGGAGAAAGAAAGCTTCACGCTGTTAATGCTGAAGAATGCAT
CACCCTCCAGGAAAGATGTGCTGTCTGAGGAATGCACAAATGGAATCATGAACTTCTTATCCAGAAAAGCA

Alignment

ORF - retro_tbel_2398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.13 %
• Parental protein coverage: 75.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TPGNLP-DSARQNYVDLVSS-LSSSPEPSSQVEPRADEKPAGYETLVVTSEDGITKIMFNRPTKKNAIST
          T.GNLP.DSARQN..DLVSS.LSSSPE..SQV.P.AD.K.A.Y.T...TSEDGITKIMFNRPTKKNA.ST
Retrocopy TLGNLPKDSARQNDLDLVSS>LSSSPESFSQVQPGADRKLAEYQT---TSEDGITKIMFNRPTKKNAAST

Parental  RMYEEIMLALKAASEDKSALTVLTGNGDYYCSGNDLTN-FTDIPPGGVEEKAKSSHILLRNFVQCFIDFP
          .MYEEI.LALKAAS.D.S..TVLTGNGDYY.SG.DLT......P.G..E....S...L.R.FV.CFIDFP
Retrocopy QMYEEIKLALKAASKDDSIITVLTGNGDYYRSGDDLTS<TNSPPGGVEERA*NSGILL-RDFVLCFIDFP

Parental  KPLIAVVNGPAVGISVTLLGLFDAVYASDRATFHTPFSALGQSPEGCSSYTFPKIMGSAKATEMLVFGKK
          KPLIAVVN.PAVG.SVTLL.LFD.VYASDRA..HTPFS.LGQSPEGCSSY.FPKIMGSAKATEMLV.GKK
Retrocopy KPLIAVVNCPAVGTSVTLLRLFDVVYASDRAMLHTPFSTLGQSPEGCSSYVFPKIMGSAKATEMLVLGKK

Parental  LTAGEACAQGLVTEVFPDSTFQREVWTRLKAYAKLPANTLRVSKNIIRSREREKLRAVNAEECITLEGRW
          LTAGEA.AQGLVTEVFPDSTFQRE.........K.P.......K.........KL.AVNAEECITL..R.
Retrocopy LTAGEAWAQGLVTEVFPDSTFQRES-IYAESICKAPSKCPENFKRGHQKQGERKLHAVNAEECITLQERC

Parental  Q-SEDCMNAIMNFLSRKA
          ..SE.C.N.IMNFLSRKA
Retrocopy A>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_2398 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2398 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,