RetrogeneDB ID: retro_tbel_4390

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_80272:1692..2936(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000003920
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000004854
• Aliases: None
• Description: None

Sequence

>retro_tbel_4390
GTGATCAGTGATGAACATGGTATCGACCCCACTGGTACCTGCCACGGGGACAGCGACCTGCAGCTGGACCGCATTTCTGC
ATACTATAAGGAAGTCACAGGTGGCAAATATGTTCCTCATGCCATCTTGGTGGATCTAGAACCTGGGACCGTGGACTCTG
TTCACTCAGGTCCTTTTGGCCAGATCTTCAGACCAGACAACTTTGTTTTTGGCCAGTCTGAGGCAGGCAGTAACTGCGCC
AAGGGCCACTGTACAGAAGGTGCTAAGCTGGTTAACTTGGTCTTGGATGTAATGCTTAAGGAGGCTGAGAGCTGTGACTG
CCTGCAGGGCTTCCAAATGACCCACTCACTGGGTGGGGGCACAGGCTCTGGAATGGGCACCCTCCTCATCAGCAAGATCT
GAGAAGAGTATCCTGACCACATCATAAATATATTCAGTGTGGCATACCCTCACCCAAGGTGTCTGACACTGTAGACAAGC
CCTACAATGTCACCCTCTCTGTCCATCAGTTGGTAGAAAACACCTTATGAGACCTACTGCATTGACAGTGAGGCTCTTTA
CGACAACTGTTTCCACACCCTCAAGGTGACCACACCAACCTATGGCGACCTGAACCACCTCGTCTCAGCCACCATGAGCA
AGGTCACCACCTGCCTCCGCTTCCCTGGCCAGCTCAGTGCTGACCTCCACAAGCTAGCCGTCAACATGGCGCACTTCCCA
CGCCTTCACTTCTTCATGCCTGGCTTTGCCACTCTCACCAGTCATGGAAGCCAGCAGTATCGAACCCTTACTGTGCCTGA
ACTCACTCAGCAGGTCTTTGAAGCCAAGAACATGATGACTGCCTATGATCCCCACCATGACTGGTACCTCACCATGGCTG
CTGTCTTCCAGGGGCAGATGTCCATGAAGGAGATAGATTAGCAGATGCTCAAAGTGAGAACAAGAACAGCTGCTACTTCA
TGGTGTGGATCCCCAACAATGTCAAGACAGCTGTCTGTGACATCCCACCTCGTGGCCTCAAGATGGCAGTCACCTTCATT
GGCACCAGCACGGCCATCCAGGAGCTTTTCAAGCACATCTCAGAGCAGTTCACTGCCATGTTCTGACAAAAGGTCTTCCT
CCACTGGTACACAGGCAAGATGGAGTTCACCGAGGCCAACAGCAACATGAACGACCCCATTTCTGAGTATCAGCAGTACC
AGGACGTCATCAAAGAAGAGGAGGAGGATTTCGGTGAGGAGGCT

Alignment

ORF - retro_tbel_4390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.38 %
• Parental protein coverage: 93.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVF
          VISDEHGIDPTG..HGDSDLQL.RI..YY.E.TG.KYVP.AILVDLEPGT.DSV.SGPFGQIFRPDNFVF
Retrocopy VISDEHGIDPTGTCHGDSDLQLDRISAYYKEVTGGKYVPHAILVDLEPGTVDSVHSGPFGQIFRPDNFVF

Parental  GQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDR
          GQS.AG.N.AKGH.TEGA.LV..VLDV..KE.ESCDCLQGFQ.THSLGGGTGSGMGTLLISKI.EEYPD.
Retrocopy GQSEAGSNCAKGHCTEGAKLVNLVLDVMLKEAESCDCLQGFQMTHSLGGGTGSGMGTLLISKI*EEYPDH

Parental  IMNTFSV-MPSP-KVSDTVVEPYNATLSVHQLVENT-DETYCIDNEALYDICFRTLKLTTPTYGDLN-LV
          I.N.FSV..P.P.KVSDTV..PYN.TLSVHQLVENT..ETYCID.EALYD.CF.TLK.TTPTYGDLN.LV
Retrocopy IINIFSVAYPHP<KVSDTVDKPYNVTLSVHQLVENT>YETYCIDSEALYDNCFHTLKVTTPTYGDLNHLV

Parental  SATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNM
          SATMS.VTTCLRFPGQL.ADL.KLAVNM..FPRLHFFMPGFA.LTS.GSQQYR.LTVPELTQQ.F.AKNM
Retrocopy SATMSKVTTCLRFPGQLSADLHKLAVNMAHFPRLHFFMPGFATLTSHGSQQYRTLTVPELTQQVFEAKNM

Parental  MAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNV-QNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFI
          M.A.DP.H..YLT.AAVF.G.MSMKE.D.QML.V..NKNS.YF..WIPNNVKTAVCDIPPRGLKM..TFI
Retrocopy MTAYDPHHDWYLTMAAVFQGQMSMKEID*QMLKV<ENKNSCYFMVWIPNNVKTAVCDIPPRGLKMAVTFI

Parental  GNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEFEE
          G.STAIQELFK.ISEQFTAMF..K.FLHWYTG.....MEFTEA.SNMND..SEYQQYQD...EEE..F.E
Retrocopy GTSTAIQELFKHISEQFTAMF*QKVFLHWYTG----KMEFTEANSNMNDPISEYQQYQDVIKEEEEDFGE

Parental  EA
          EA
Retrocopy EA

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_4390 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4390 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017637	1 retrocopy	retro_cjac_1649,
Erinaceus europaeus	ENSEEUG00000002955	1 retrocopy	retro_eeur_441,
Myotis lucifugus	ENSMLUG00000016179	1 retrocopy	retro_mluc_401,
Tupaia belangeri	ENSTBEG00000004854	9 retrocopies	retro_tbel_2291, retro_tbel_3456, retro_tbel_3944, retro_tbel_4113, retro_tbel_413, retro_tbel_4390 , retro_tbel_4439, retro_tbel_961, retro_tbel_962,
Tarsius syrichta	ENSTSYG00000003440	2 retrocopies	retro_tsyr_1068, retro_tsyr_2125,
Tursiops truncatus	ENSTTRG00000006144	1 retrocopy	retro_ttru_1393,