RetrogeneDB ID: retro_tbel_306

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1696:16620..17118(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCHL1
• Ensembl ID: ENSTBEG00000011438
• Aliases: None
• Description: ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) [Source:HGNC Symbol;Acc:12513]

Sequence

>retro_tbel_306
TATGAAGTATTCAGAACAGAAGAGGAGGAAAAAATAAAATCTCAGGGGCAGGCTGTTACATCATCAGTATATTTCATGAA
GCAAACAATCAGTCATGCCTGTGGAATAATTGGACTGATCCACACTATTGCAAACAATAAAGACAAGATGCACTTTGAAT
CTGGATCAACCTTGAAAAAATTCCTCGAAGAGTCTGTGTCAATGAGCCCTGAAGAGCAAGCCAAATACCTGGAGAACTAT
GACGCAATTCAAGTTACTCATGAAACCAGTGCACATGAAGGTCAGACTGAGGCACTAAATGTAGATGGAAAAGTAGATCT
TCATTCTATTGCATTAATTCATATAGATGGGCATCTCTATGAATGAGGTGGGTGGAAACCATTTCCAATTAACCATGGGA
AAACTAGTGATGAAACTTTACTGGAAGTTGCCATAGAAGTTTGCAAGAAGTTTATGGAACATGACTCTGATGAACTAAGA
TTCAACACGATTGCTCTT

Alignment

ORF - retro_tbel_306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.81 %
• Parental protein coverage: 97.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HENFRKKQIEELK--GQEVSPKVYFMKQTIGNACGTIGLIHAVANNQDKLQFEDGSVLKQFLSETEKMSP
          .E.FR....E..K..GQ.V...VYFMKQTI..ACG.IGLIH..ANN.DK..FE.GS.LK.FL.E...MSP
Retrocopy YEVFRTEEEEKIKSQGQAVTSSVYFMKQTISHACGIIGLIHTIANNKDKMHFESGSTLKKFLEESVSMSP

Parental  EDRAKCFEKNEAIQAVHDAVAQEGQ---CRVDDKVNFHFILFNNVDGHLYELDGRMPFPVNHGTSSDDSL
          E..AK..E...AIQ..H...A.EGQ.....VD.KV..H.I.....DGHLYE..G..PFP.NHG..SD..L
Retrocopy EEQAKYLENYDAIQVTHETSAHEGQTEALNVDGKVDLHSIALIHIDGHLYE*GGWKPFPINHGKTSDETL

Parental  LQNAAKVCREFTEREQGEVRFSAVAL
          L..A..VC..F.E....E.RF...AL
Retrocopy LEVAIEVCKKFMEHDSDELRFNTIAL

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_306 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_306 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003295	1 retrocopy	retro_chof_1737,
Callithrix jacchus	ENSCJAG00000019346	1 retrocopy	retro_cjac_365,
Echinops telfairi	ENSETEG00000012347	1 retrocopy	retro_etel_44,
Felis catus	ENSFCAG00000025457	1 retrocopy	retro_fcat_1321,
Macropus eugenii	ENSMEUG00000013774	1 retrocopy	retro_meug_8,
Oryctolagus cuniculus	ENSOCUG00000001353	1 retrocopy	retro_ocun_309,
Ictidomys tridecemlineatus	ENSSTOG00000015507	1 retrocopy	retro_itri_288,
Tupaia belangeri	ENSTBEG00000011438	1 retrocopy	retro_tbel_306 ,
Tursiops truncatus	ENSTTRG00000012095	1 retrocopy	retro_ttru_1370,