RetrogeneDB ID: retro_tbel_2328

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_109097:11960..13128(+)
• 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_2328
GAAGAAGTTTTAAAGGATTTTGAAGACTTGGCTGGAAAACTTCCATGATCAGACCCTCTAAAAGTATGGAAAATTAATAC
CAGTTTCAAGAAAAGAAAAAGTACAAAAAGATTAATCAGAATTCAAATAAAGACTGAAAATGGGCAAGGAGACAAACTAG
ATGAGAGGGATGTTAAAAAAGATTCCACTAGCAATGCTTTAGACTCACATATTTTGGACTATTATAAAAACCCGGCCATC
AAAGAAGAGGTGTCAACATTAGTAGGTGATGATTTGGCATCTTGTAAAGATGAGACTGATGAAAACACAAAAGAAGAAAC
AGAGCCTGAAATGATAAAATTCAGAGTCACATGCAATAGGGCAGGAGAGAAACACTGCTTTACCTCAAGTGAGGCTGCAA
GAGATTTTGGGGGTGCTGTTCAAGATCACTTTTAAGTGGAAGGCAGATATGACCAACTTTGATGTAGAGGTTCTTTTAAA
TATCCTTGATAATGAAGTCATTGTGGGAATTGCTTTGACTGAAGAGAGTCTCCACCGAAGAAGTAGCACACATTTTGGAC
CCACAACCCTCATGTAAATTCTTGCCTATGGGATGCTCAGACTCTGTGCTCAACCTACTGATATAATAGTTGATCCAATG
TGTGGAACGGGGGCAATACCAATAGAGGGTGCTACAGAATGGTCTAACTGTTACCATATTGCTGGTGATAATAATCCATT
GGCTGTGAACCGAGCAGCAAATAACATCTCATCTTTATTGACCAAGAGTCAAATTAAAGAAGGTGAACCCTCCTGGGGCT
TGCCCATAGATGCTTTTCAGTGGGATATCTGCAATCTGCCACTGAGAACTGGCTCTGTGGATATTATTGTAACAGATATG
CCATTTGGAAAAAGGATGGGCTCCAAAAAGAGAAACTGGAACATTTATCCAGCATGCCTACAAGGGATGAGCCACATCTG
TAGACCTGGAAAAGGCCGAGCTGTCCTACTTACTCAGGACAAGAAATGCTTTACCAAGACATTATCTGGAATAGGACATG
TATGGCGAAAGGTGCATACAGTCTGGGTGGACATAGGAGGTCTTCATGCTGCAGTTTATCTTCTGAAACGCACACCTCAA
GCTTTTGCTTATCCTTCAGAAGAAGATGGAGGAAGAGGAACTCCTTGG

Alignment

ORF - retro_tbel_2328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.65 %
• Parental protein coverage: 77.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEVLKDFEDLAGKLPWSDPLKVWKINTS-FKKRKTKRKKINQNSNKGK-TENGQGDKLDERDVKKDSTNN
          EEVLKDFEDLAGKLP.SDPLKVWKINTS.F...K.K.KKI..N.N..K.TENGQGDKLDERDVKKDST.N
Retrocopy EEVLKDFEDLAGKLP*SDPLKVWKINTS<FQEKK-KYKKI--NQNSNK>TENGQGDKLDERDVKKDSTSN

Parental  ALDSHILDYYENPAIKEEVSTLVGDDLASCKDETDENTKEETEPQVIKFRVTCNRAGEKHCFTSNEAARD
          ALDSHILDYY.NPAIKEEVSTLVGDDLASCKDETDENTKEETEP..IKFRVTCNRAGEKHCFTS.EAARD
Retrocopy ALDSHILDYYKNPAIKEEVSTLVGDDLASCKDETDENTKEETEPEMIKFRVTCNRAGEKHCFTSSEAARD

Parental  FGGAVQDHF-KWKADMTNFDVEVLLNIHDNEVIVGIALTEESLHRRNITHFGPTTLRSTLAYGMLRLCAP
          FGGAVQDHF.KWKADMTNFDVEVLLNI.DNEVIVGIALTEESLHRR..THFGPTTL...LAYGMLRLCA.
Retrocopy FGGAVQDHF>KWKADMTNFDVEVLLNILDNEVIVGIALTEESLHRRSSTHFGPTTLM*ILAYGMLRLCA-

Parental  QPTDI--DPMCGTGAI-IEGATEWSNCYHIAGDNNPLAVNRAANNISSLLTKSQIKEGKPSWGLPIDAVQ
          QPTDI..DPMCGTGAI.IEGATEWSNCYHIAGDNNPLAVNRAANNISSLLTKSQIKEG.PSWGLPIDA.Q
Retrocopy QPTDIIVDPMCGTGAIPIEGATEWSNCYHIAGDNNPLAVNRAANNISSLLTKSQIKEGEPSWGLPIDAFQ

Parental  WDICNLPLRTGSVDIIVTDMPFGKRMGSKKRNWNLYPACLQEMSRVCRPGTGRAVLLTQDKKCFTKALSG
          WDICNLPLRTGSVDIIVTDMPFGKRMGSKKRNWN.YPACLQ.MS..CRPG.GRAVLLTQDKKCFTK.LSG
Retrocopy WDICNLPLRTGSVDIIVTDMPFGKRMGSKKRNWNIYPACLQGMSHICRPGKGRAVLLTQDKKCFTKTLSG

Parental  -GHVWRKVHTVWVNIGGLHAAVYLLKRTPQAFACPSEEDRGRGTPW
          .GHVWRKVHTVWV.IGGLHAAVYLLKRTPQAFA.PSEED.GRGTPW
Retrocopy IGHVWRKVHTVWVDIGGLHAAVYLLKRTPQAFAYPSEEDGGRGTPW

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_2328 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2328 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,