RetrogeneDB ID: retro_tbel_2365

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_109580:111356..113164(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000015361
• Aliases: None
• Description: None

Sequence

>retro_tbel_2365
GTGCTGGAGAATGCTGAAGGTGCCAGACACCACCCCTTCTGTTGTGGCAATTACAGCAGATGGTGAGCCACTTGTTGGCA
TGCCTGCCAAGGGACAGGCTGTCACCGATCCAAACAATACATTCTGTGCCACCAAGCATCTCATTGGCCAACAATATGAT
GAACCGGAAGTACAGAAAGACATCAAAAACTTTCCCTTTAAAATTGTCCACGCCTCCAATGGTGATGCCTGGGTTGAGGC
TCATGGAAAACCCTATTCTCCAAGTCAGGCTGGAGCATTTGTGTTGATGAAGATGAAAGAAACCAGAAAATTACTTGGGG
CATACAGCAAAAATTGCTGTGATCACAGTCCCAGCTTATTTCAATGATCCACAGAGACGGGCTACTAAGGATGCTGGGCA
GACATCTGGACTAAATGTGCTTAGAGTGATTAACAAACCCATAGCTGCTGTTCTGGCTTGTGGTCTAGACAAATCAGAAG
ACAAAGTCATGGCTGTATATGACTTAGGTGGTGGGACTTTTGATATTTCTATCCTGGAAATCCAGAAAGGGGTATTTGAG
GTGAAATCTACCAATGGGGACACTTTCTTAGGTGGCAAAGACTTTGACCAGGCCTTGCCACAACACACTGTGAAAGAGTT
CAAGAGAGAGACAGGGGTAGATTTGACCAAAGACAACATGGCCCTTCAGAGGGTTTGTGAAGCTGCTGAGAAGGCGAAGT
GTGAACTCTCCTCTTCTGTTCAGACTGACATAAATTTGCCGTATCTTACAATGGATGCTTCTGGACCCAAACATTTGAAT
ATGAAGCTGACCCGGGCTCAATTTGAGGGGATTGTCACTGACCTAATCAGGAGGACTATTGCTCCATGCCAGAAAGCTAT
GCAAGATGCAGAAGTCAGCCAGAGTGACATAGAAGAAGTGATTCTTGTTGGTGGCATGACTAGGATGCCTAAGGTTCAGC
AGACTGTGCAGGATCTTTTTGGCAGAGCCCCAAGTAAAGCTGTCAATCCTGATGAGGCTGTAGCCATTGGTGCTGCCATT
CAGGGAGGTGTGTTGGCTGGTGATGTCACAGATGTATTGCTCCTGGATGTCACTCCCCTGTCTTTGGGTATTGAGACTCT
TGGAGGTGTCTTTACCAAACTTATCAACAGAAACACCACTATTCCAACCAAGAAAAGTCAGGTGTTTTCTACTGCTGCCG
ATGGACAGACTCAAGTGGAGATTAAAGTGTGTCAGGGTGAGAGAGAGATGACTGGTGACAACAAACTTCTTGGACAGTAT
ACTTTGATTGGAAATCCCCCAGTTCCTCGTGGAGTCCCTCAGATTGAAGTTACATTTGGCATTGATGCCAATGGGATTGT
ACATGTTTCTGCTAAGGATAAGGGCACAGGACATGAGCAGTAGATTGTAATACAGTGTTCTGGTGGATTAAGCAAAGATG
ATATTGAAAATATGGTTAAAAATGCAGAGAAGTATGCCGAAGAAGACCGGTGAAAGAAGGAACGAGTTGAAGCAGTTAAT
ATGGCTGAACGAATCATTCATGACACAGAAACCAAGATGGAAGAATTCAAGGACCAATTGCCTACAGATGAGTGCAACAA
GCTGAAAGAAGAGATTTCCAAAATGAGGGAGCTCCTGGCTCGAAAAGACAGTAAAACAGGAGAAAACATGAGGCAGGCAG
CATCCTCCCTTCGGCAGCCATCACTGAAGCTCTTTGAAATGGCATACAAAAAGATGGCATCTGAGCGAGAAGGCTCTGGA
AGTTCTGGTACTGGGGAACAAAAGGAAGATCAAAAGGAAGAAAAACAG

Alignment

ORF - retro_tbel_2365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.92 %
• Parental protein coverage: 88.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLENAEGAR-TTPSVVAFTADGERLVGMPAKRQAVTNPNNTFYATKRLIGRRYDDPEVQKDIKNVPFKIV
          VLENAEGAR.TTPSVVA.TADGE.LVGMPAK.QAVT.PNNTF.ATK.LIG..YD.PEVQKDIKN.PFKIV
Retrocopy VLENAEGAR>TTPSVVAITADGEPLVGMPAKGQAVTDPNNTFCATKHLIGQQYDEPEVQKDIKNFPFKIV

Parental  RASNGDAWVEAHGKLYSPSQIGAFVLMKMKETAENYLG-HTAKNAVITVPAYFNDSQRQ-TKDAGQISGL
          .ASNGDAWVEAHGK.YSPSQ.GAFVLMKMKET....LG.HTAK.AVITVPAYFND.QR..TKDAGQ.SGL
Retrocopy HASNGDAWVEAHGKPYSPSQAGAFVLMKMKET-RKLLG>HTAKIAVITVPAYFNDPQRRATKDAGQTSGL

Parental  NVLRVINEPTAAALAYGLDKSEDKVIAVYDLGGGTFDISILEIQKGVFEVKSTNGDTFLGGEDFDQALLQ
          NVLRVIN.P.AA.LA.GLDKSEDKV.AVYDLGGGTFDISILEIQKGVFEVKSTNGDTFLGG.DFDQAL.Q
Retrocopy NVLRVINKPIAAVLACGLDKSEDKVMAVYDLGGGTFDISILEIQKGVFEVKSTNGDTFLGGKDFDQALPQ

Parental  HIVKEFKRETGVDLTKDNMALQRVREAAEKAKCELSSSVQTDINLPYLTMDASGPKHLNMKLTRAQFEGI
          H.VKEFKRETGVDLTKDNMALQRV.EAAEKAKCELSSSVQTDINLPYLTMDASGPKHLNMKLTRAQFEGI
Retrocopy HTVKEFKRETGVDLTKDNMALQRVCEAAEKAKCELSSSVQTDINLPYLTMDASGPKHLNMKLTRAQFEGI

Parental  VTDLIRRTIAPCQKAMQDAEVSKSDIGEVILVGGMTRMPKVQQTVQDLFGRAPSKAVNPDEAVAIGAAIQ
          VTDLIRRTIAPCQKAMQDAEVS.SDI.EVILVGGMTRMPKVQQTVQDLFGRAPSKAVNPDEAVAIGAAIQ
Retrocopy VTDLIRRTIAPCQKAMQDAEVSQSDIEEVILVGGMTRMPKVQQTVQDLFGRAPSKAVNPDEAVAIGAAIQ

Parental  GGVLAGDVTDVLLLDVTPLSLGIETLGGVFTKLINRNTTIPTKKSQVFSTAADGQTQVEIKVCQGEREMA
          GGVLAGDVTDVLLLDVTPLSLGIETLGGVFTKLINRNTTIPTKKSQVFSTAADGQTQVEIKVCQGEREM.
Retrocopy GGVLAGDVTDVLLLDVTPLSLGIETLGGVFTKLINRNTTIPTKKSQVFSTAADGQTQVEIKVCQGEREMT

Parental  GDNKLLGQFTLIGIPPAPRGVPQIEVTFDIDANGIVHVSAKDKGTGREQQXXXXXXXXXXXDDIENMVKN
          GDNKLLGQ.TLIG.PP.PRGVPQIEVTF.IDANGIVHVSAKDKGTG.EQ............DDIENMVKN
Retrocopy GDNKLLGQYTLIGNPPVPRGVPQIEVTFGIDANGIVHVSAKDKGTGHEQ*IVIQCSGGLSKDDIENMVKN

Parental  AEQYAEEDRRKKERVEAVNMAEGIIHDTETKMEEFKDQLPADECNKLKEEISKMRELLARKDSETGENIR
          AE.YAEEDR.KKERVEAVNMAE.IIHDTETKMEEFKDQLP.DECNKLKEEISKMRELLARKDS.TGEN.R
Retrocopy AEKYAEEDR*KKERVEAVNMAERIIHDTETKMEEFKDQLPTDECNKLKEEISKMRELLARKDSKTGENMR

Parental  QAASSLQQASLKLFEMAYKKMASEREGSGSSGTGEQKEDQKEEKQ
          QAASSL.Q.SLKLFEMAYKKMASEREGSGSSGTGEQKEDQKEEKQ
Retrocopy QAASSLRQPSLKLFEMAYKKMASEREGSGSSGTGEQKEDQKEEKQ

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_2365 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2365 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000014493	1 retrocopy	retro_dord_304,
Macropus eugenii	ENSMEUG00000016000	1 retrocopy	retro_meug_953,
Ornithorhynchus anatinus	ENSOANG00000002817	1 retrocopy	retro_oana_82,
Tupaia belangeri	ENSTBEG00000015361	1 retrocopy	retro_tbel_2365 ,
Tarsius syrichta	ENSTSYG00000011769	1 retrocopy	retro_tsyr_2147,
Vicugna pacos	ENSVPAG00000006332	1 retrocopy	retro_vpac_524,