RetrogeneDB ID: retro_tbel_2009

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_651:160018..161060(-)
• Located in intron of: ENSTBEG00000001785

Retrocopy information

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

Parental gene information

• Parental gene symbol: DBNL
• Ensembl ID: ENSTBEG00000004139
• Aliases: None
• Description: drebrin-like [Source:HGNC Symbol;Acc:2696]

Sequence

>retro_tbel_2009
CCCAAGTTCGTCCTTATCAACTGGATGGGCAAGGGTGTGAAGGACGAGTGGAAGGGAGTATGCACCTGTCACATCAGCAC
TGGGGCCAGCTTCCTGAAGGGGGCCCATGTGACCATGGATGCATGGGCCTAGAGAACTTGGAGCTCGAGTGCATCTTGCA
GAAGGTAGCCAAGGCATCTGCTGCTAAATACAGCTTCCACAGGGAGGACAGCTGCTTCCAGGACACGGGGCCCAGGCCCT
GTGGGCTCTGTGTACCAGAAGACTAATGCTGTCTCAGAGATCAAAAGAGTCGGCAAAGACAGTTTCTGGGCCAAAGCAGA
AAAAAAGGAAAATAAACCCCGGCTGGAGGAAGAGGAGCAGCAGTGGCTGGAACAAGACTGCTAGGAGTGGGAGCTGTGAG
AAGCTGCACAGCAAGAGCAGCGCTTTCGGAAGCAGGGTGCCTACAGACCCAAGAAGCAGCAGCAGCAGGATGTGATCCCA
GGGAGCTGCATGGAACTGGAACCTGCTGGCCAGTGGGCTATGCACCCAAGGGAGGTTTGCCAGCAGAAGGAGAGGGCCAC
ATCTACCACCTCTGCTCCCAGCTCCTCAGCCAGGCAAGCTGAGGAGCTCCTTCCTGCAGAAGCAGCTCAAACAGACACCC
AGTGCCAGAGAGCAGCTCCAACTCTCATCACCTAAAGGCCTAGGGCAGATCTCTGTGAGTGGCCAACACCCAACACCACT
CCATGTCTGTTCCAGGCAGAAGAGGAGATTGTCTTCGAGGAACCCCTGGAGCAGGAGATCCTTTATGAGGAGGCTACTCT
GGTGTAGCAGCCAGGGACCAGCTCTGAGCTGGTCGAGTCCTATACATGGGGTTGGGTGTTCAGTGGGCAGGGGCTATGTG
CCCAGGTCCTGTACCACTACCAGGCAACTGATGACACAGAGATCTTCTTTGACCCTGAGAATCTCATAACAGGCATTGAG
GTGATGGAGAGGACCGGTGGTGTGGCTACAGGCGGATGGCCACTTTGACATGTTCTCAGCCAATTATGTGGAGCTCCTTG
AG

Alignment

ORF - retro_tbel_2009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.75 %
• Parental protein coverage: 82.53 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PKFVLINWTGEGVNDVRKGVCANHVSTMANFLKGAHVTINARA-EEDVEPESIMQKVAKASGANYSFHKE
          PKFVLINW.G.GV.D..KGVC..H.ST.A.FLKGAHVT..A.A..E..E.E.I.QKVAKAS.A.YSFH.E
Retrocopy PKFVLINWMGKGVKDEWKGVCTCHISTGASFLKGAHVTMDAWA<LENLELECILQKVAKASAAKYSFHRE

Parental  GSRFQDT-GPQAPVGSVYQKTNAVSEIKRVGKDSFWAKAEKEEENRRLEERRRAEEEQRRLEQERQEREL
          .S.FQDT.GP..PVGSVYQKTNAVSEIKRVGKDSFWAKAE...EN......R..EEEQ..LEQ...E.EL
Retrocopy DSCFQDT>GP-GPVGSVYQKTNAVSEIKRVGKDSFWAKAE-KKEN----KPRLEEEEQQWLEQDC*EWEL

Parental  REAAQREQRYREQSARSRPEQQQQDVIPEGRTEQTCVSEPAGQRAVHPREVFQQKERAMSTTSVPS-PQP
          .EAAQ.EQR.R.Q.A..RP..QQQ.....G........EPAGQ.A.HPREV.QQKERA.STTS.PS.PQP
Retrocopy *EAAQQEQRFRKQGAY-RPKKQQQQDVIPGSCMEL---EPAGQWAMHPREVCQQKERATSTTSAPS>PQP

Parental  GKLRSPFLQKQLTQPEAPSTREP-APTPIISGPRAGKLG-PASSATPYLVQAEEETVYEESPEQEALYEE
          GKLRS.FLQKQL.Q...PS.RE..APT.I...PRA.....P....TP.L.QAEEE.V.EE..EQE.LYEE
Retrocopy GKLRSSFLQKQLKQ--TPSAREQ<APTLIT*RPRADLCEWPTPNTTPCLFQAEEEIVFEEPLEQEILYEE

Parental  PPQVQQPGTGSEQVNPHTEGRVFGGQGLCARALYDYQAADDTEISFDPENLITGIEVID-EGWWRGY-GP
          ...V.QPGT.SE.V...T.G.VF.GQGLCA..LY.YQA.DDTEI.FDPENLITGIEV...E..W.GY...
Retrocopy ATLV*QPGTSSELVESYTWGWVFSGQGLCAQVLYHYQATDDTEIFFDPENLITGIEVME<EDRWCGY<QA

Parental  DGHFGMFPANYVELLE
          DGHF.MF.ANYVELLE
Retrocopy DGHFDMFSANYVELLE

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_2009 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2009 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017502	1 retrocopy	retro_amel_1510,
Tupaia belangeri	ENSTBEG00000004139	1 retrocopy	retro_tbel_2009 ,