RetrogeneDB ID: retro_tbel_4165

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_69554:792..1201(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000012901
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ECHS1
• Ensembl ID: ENSTBEG00000008062
• Aliases: None
• Description: enoyl CoA hydratase, short chain, 1, mitochondrial [Source:HGNC Symbol;Acc:3151]

Sequence

>retro_tbel_4165
ATGGCAGCGCTACATGCCTTGCTACCCTTAGTCCGCCTACAGCTGCACCCCGCAGCCTGCTGCTACGCCTTGCGTTCCCT
TGCCTTGGGTGCTTTCAATACATCATCGCAGAGAAAAGAGGGAAAAATAACAATGAGGGATTGATCCAACTGAATCACCC
CAACGCACTTAATGTACTCTGCGATGGCCTGACAGAGGAGCTCGACCAGGCACTGGAGACCTTCAAGAAGGACCCAGCCA
TGGGGGCCACTGTCCTTACTGGTGGGGATAAGGTAATTGCAACTGGGACTGATATCAAGGAAATGCAGAACTCGACGTTC
CAAGATTGTTACTCTGGCAAGTTCTTGAGCCACGGGACCAGCTCACCCGCGTCCAGAAACCAGTCATAGCTGCTGTCGAT
GGTTATGCT

Alignment

ORF - retro_tbel_4165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.57 %
• Parental protein coverage: 56.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAALRALLPLLRIQLRPAARCYALRSFASGANFQYIIAEKRG-KNNNVGLIQLNRPKALNALCSGLIEEL
          MAAL.ALLPL.R.QL.PAA.CYALRS.A.GA.F......K.G.KNNN.GLIQLN.P.ALN.LC.GL.EEL
Retrocopy MAALHALLPLVRLQLHPAACCYALRSLALGA-FNTSSQRKEG<KNNNEGLIQLNHPNALNVLCDGLTEEL

Parental  NQVLETFEKDPAVGAVVLTGGDKAFAAGADIKEMQNQTFQDCYSGKFLSHW-DQLSRFQKPVIAAVNGYA
          .Q.LETF.KDPA.GA.VLTGGDK..A.G.DIKEMQN.TFQDCYSGKFLSH..DQL.R.QKPVIAAV.GYA
Retrocopy DQALETFKKDPAMGATVLTGGDKVIATGTDIKEMQNSTFQDCYSGKFLSHG<DQLTRVQKPVIAAVDGYA

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_4165 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4165 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
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,