RetrogeneDB ID: retro_tbel_1981

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_6105:112874..113514(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNL1
• Ensembl ID: ENSTBEG00000017328
• Aliases: None
• Description: thioredoxin-like 1 [Source:HGNC Symbol;Acc:12436]

Sequence

>retro_tbel_1981
TGTGGACCATGTTTGAGGATTGCCCTGGCATTCAGGGCAATGAATAATAAATAGCTTCAGGCTGTTTTCTTAGCGGTAGA
TGTGCATCAGTGTCAGGGAACAGTTGCCACCGATAATACATTAGTAACACCTACATTTTTGTTTTTCTGAAACAAATGAG
AATTGATCAGTATCAAGGAGCAGGTGTGTGGGATTAGAAGAAAAAGTCAAATGACACTTAGAAAATGACCCTGGAAGCAA
TGAAGACATAGATATTCCAAAAGGATATATGGATTCGATGTCATTTCTTTACAAAGCTGGGTTGTGAGTGTCAATGAAAA
GCGATGAAAATGGATTTGACAAGTGTTTACAAAAACACCTGAGCTTCTTGGAATCTGCCTGTGATGAACAGCTACTTATT
TACCATGACATCCAATCAACCTGTTAAGCTTTTATTCCATGAAATTTCGAGGGCCAGATAATGGCTAGGGTCGTAAACAT
GTAAAAATTTTTATCAACCCTCTTTCATTGATGGATTTTGAAGAGGCAGAAAAAAAGTGAACCAACTCAAGCTCTGGAAC
TGGCAGAGGATGATACTGAAGACGGCATTCCTTCTGTTAAGTTTCAGAATGCTAACAGTATATCTCTATTTGTTCAGTCC

Alignment

ORF - retro_tbel_1981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.17 %
• Parental protein coverage: 87.85 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  CGPCLRIAPAFSSMSNKYPQAVFLEVDVHQCQGTAATNNISATPTFLFFRNK-VKIDQYQGADA-VGLEE
          CGPCLRIA.AF..M.NK..QAVFL.VDVHQCQGT.AT.N...TPTFLFF.NK...IDQYQGA...VGLEE
Retrocopy CGPCLRIALAFRAMNNK*LQAVFLAVDVHQCQGTVATDNTLVTPTFLFF*NK<MRIDQYQGAGV<VGLEE

Parental  KIKQHLENDPGSNEDTDIPKGYMDLMPFINKAGCECLNESDENGFDNCLRKDLSFLESDCDEQLLI-TXX
          K.K.HLENDPGSNED.DIPKGYMD.M.F..KAG......SDENGFD.CL.K.LSFLES.CDEQLLI.T..
Retrocopy KVK*HLENDPGSNEDIDIPKGYMDSMSFLYKAGL*VSMKSDENGFDKCLQKHLSFLESACDEQLLI>TMT

Parental  XNQPVKL-YSMKFQGPYNGQGPKYVKIFINLPRSMDFEEAE-RSEPTQALELTEDDIKEDGIVPLRYVKF
          .NQPVKL.YSMKF.GP.NG.G.K.VKIFIN....MDFEEAE..SEPTQALEL.EDD..EDGI.....VKF
Retrocopy SNQPVKL>YSMKFRGPDNG*GRKHVKIFINPLSLMDFEEAE>KSEPTQALELAEDD-TEDGIPS---VKF

Parental  QNVNSVTIFVQS
          QN.NS...FVQS
Retrocopy QNANSISLFVQS

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_1981 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1981 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000137	1 retrocopy	retro_cfam_875,
Choloepus hoffmanni	ENSCHOG00000010262	1 retrocopy	retro_chof_1723,
Ictidomys tridecemlineatus	ENSSTOG00000000075	2 retrocopies	retro_itri_302, retro_itri_414,
Tupaia belangeri	ENSTBEG00000011193	2 retrocopies	retro_tbel_1293, retro_tbel_3405,
Tupaia belangeri	ENSTBEG00000017328	2 retrocopies	retro_tbel_1981 , retro_tbel_911,
Tursiops truncatus	ENSTTRG00000001161	1 retrocopy	retro_ttru_1154,