RetrogeneDB ID: retro_tbel_4489

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_85481:10302..11205(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THUMPD3
• Ensembl ID: ENSTBEG00000003450
• Aliases: None
• Description: THUMP domain containing 3 [Source:HGNC Symbol;Acc:24493]

Sequence

>retro_tbel_4489
ATTGAAGAAGAGGTGTTAACATTAGTAGGTGAGACTGATGAAAACACAAAAGAAGAAACAGAGCCTCAAGTGATAAAATT
CAGAGTCACATGCAGTGGGGCAGGAGAGAAACACTGCTTTACCTCAAATGAGGCTGCAAGAGATTGTAGGGGTGCTGTTC
AAGATCACTTTAAGTGGAAGGCCAATATGACCAGCTTTGATGTAGAGGTTCTTTTAAATATCCATGATAATGAAGTCATT
GTGGGAATTACTTTGACTGAAGAGAGTCTCCACCGAAGAAATATTATACATTTTGGACCCACAACCCTCAGGTAAATTCT
TGCCTATGGGATGCTCAGACTCTGTGCTCCTCAACCTACTGATATAATAGTTGATCCAATGTGTGGAAGGGGGGCAATAC
CAATAGAGGGTGCTACAGAATGGTCTAACTGTTACCATATTGCTGGTGATAATAATCCATTGGCTGTGAATCGAGCAGCA
AATAACATCTCATCTTTATTGACCAAGAGTCAAATTAAAGAAGGCAAATCCTCCTGGGTCTTGCCCATAGATGCTTTTCA
GTGGGATATCTGCAATCTGCCACTAAGAACTGTGGATATTATTGTAACAGATATGCCATTTGGAAAAAGGATGGGCTCCA
AAAAGAGAAACTGGAACCTTTATCCAGCATGCCTACAAGAGATGAACTGCATCTGTAGACCTGGAACAGGCCGAGCTGTC
CTACTTACTCAGGACAAGAAATGCTTTACCAAGACATTATCTGGAATGGGACATGTATGGCAAAAGGTGCATACAGTCTG
GGTGAACATAGGGGGTCTTCATGCTGCAGTTTACCTTCTGAAATGCACACCTCAAGCTTTTGCTTGTCCTTCAGAAGAAG
ATGGAGGAAGAGGAACTCCTTGG

Alignment

ORF - retro_tbel_4489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.79 %
• Parental protein coverage: 59.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGDDLASCKDETDENTKEETEPQVIKFRVTCNRAGEKHCFTSNEAARDFGGAVQDHFKWKADMTNFDVEV
          ..........ETDENTKEETEPQVIKFRVTC..AGEKHCFTSNEAARD..GAVQDHFKWKA.MT.FDVEV
Retrocopy IEEEVLTLVGETDENTKEETEPQVIKFRVTCSGAGEKHCFTSNEAARDCRGAVQDHFKWKANMTSFDVEV

Parental  LLNIHDNEVIVGIALTEESLHRRNITHFGPTTLRSTLAYGMLRLCAPQPTDI--DPMCGTGAI-IEGATE
          LLNIHDNEVIVGI.LTEESLHRRNI.HFGPTTLR..LAYGMLRLCAPQPTDI..DPMCG.GAI.IEGATE
Retrocopy LLNIHDNEVIVGITLTEESLHRRNIIHFGPTTLR*ILAYGMLRLCAPQPTDIIVDPMCGRGAIPIEGATE

Parental  WSNCYHIAGDNNPLAVNRAANNISSLLTKSQIKEGKPSWGLPIDAVQWDICNLPLRTGSVDIIVTDMPFG
          WSNCYHIAGDNNPLAVNRAANNISSLLTKSQIKEGK.SW.LPIDA.QWDICNLPLRT..VDIIVTDMPFG
Retrocopy WSNCYHIAGDNNPLAVNRAANNISSLLTKSQIKEGKSSWVLPIDAFQWDICNLPLRT--VDIIVTDMPFG

Parental  KRMGSKKRNWNLYPACLQEMSRVCRPGTGRAVLLTQDKKCFTKALSG-GHVWRKVHTVWVNIGGLHAAVY
          KRMGSKKRNWNLYPACLQEM...CRPGTGRAVLLTQDKKCFTK.LSG.GHVW.KVHTVWVNIGGLHAAVY
Retrocopy KRMGSKKRNWNLYPACLQEMNCICRPGTGRAVLLTQDKKCFTKTLSGMGHVWQKVHTVWVNIGGLHAAVY

Parental  LLKRTPQAFACPSEEDRGRGTPW
          LLK.TPQAFACPSEED.GRGTPW
Retrocopy LLKCTPQAFACPSEEDGGRGTPW

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_4489 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4489 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 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000008538	1 retrocopy	retro_mluc_1991,
Macaca mulatta	ENSMMUG00000017307	1 retrocopy	retro_mmul_1600,
Otolemur garnettii	ENSOGAG00000017111	1 retrocopy	retro_ogar_3452,
Sus scrofa	ENSSSCG00000030273	1 retrocopy	retro_sscr_873,
Tupaia belangeri	ENSTBEG00000003450	7 retrocopies	retro_tbel_2328, retro_tbel_2589, retro_tbel_3717, retro_tbel_4362, retro_tbel_4489 , retro_tbel_4567, retro_tbel_969,