RetrogeneDB ID: retro_tbel_1535

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5033:47677..48687(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000000416
• Aliases: None
• Description: None

Sequence

>retro_tbel_1535
GGTGGTATCACAGCCGTCACCGTGAACAAGAGCCTGCTGAACCCCCTTAAGCTAGAGGTGGACCCCAACATACAGGCCAT
GCGCACCCAGGAAAAGGAGCAGATCAAGACCCTCAACAAGTTCGCCTCCTTCATCGACAAGGTCCGGTTCCTTGAGCAGC
AGAACAAGATGCTGGAGACCAAGTGGAGCCTCCTGCAGCAGCAGAAGACAGCCCGGAGCAACATGGACAACATGTTCAAG
AGCTACATCAACAACCTGCACCGGCAGCTGGACACCCTGGGCCAGGAGAAGCTGAAGCTGGAGGCGGAGCTTGGCAACAT
GCAGGGGCTGGTGGAGGACTTCAAGAAGAAGTACGAGGATGAGATCATGAAGCGTACAGAGATGGAGAATGAATTCGTCA
TCATCAAGAAGGACGTGGATGAAGCTTACATGAACAAGGTAGAGCTGGATTCTCGCCTGGAAGGGCTCACTGATGAGATC
AACTTCCTCAGGCAGCTATATGAAGAGGAGATCCGCGAGCTGCAGTCCCAGATCTCCGACATGTCCGTGGTCCTGTCCAT
GGACAACAGCTGCTCCTGGACATGGACGGCATCATTGCCCAGGTCCGCGCCCAGTATAAGGAAATCGCCAACCGCAGCCG
GGCTGAAGTTGAGAACATGTACAAAATCAAGTATGAGGAGCTGTAGACGCTGGCTGGGAAGCACAGGGATGACCTGCGGC
GCACGAAGACTGAAATCTCTGAGATGAACAGGAGCATTAGCCGGCTCCAGGCTGAGATTGAGGGCCTTAAGGGCCAGAGA
GCGTCCATGGAGGCCGTCATTGCTGATGCTGAGCAGCGCGGGGAGCTGGCCATTAAGGACGCCGACGCCAACGCCAAGCT
GGCTCAGCTGGAGGCAGCTCTGCAGCAGGCCAAGCAGGACATGTCGCGGCAGCTGCGCGAGTACCAGGAGCTCACGAACG
TCAAGCTGGCCCTGGACATCGAGATCGCTACCTACCGCAAGTTGCTGGAG

Alignment

ORF - retro_tbel_1535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.4 %
• Parental protein coverage: 71.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGIQEVTINQNLLTPLNLQIDPTIQRVRTEEREQIKTLNNKFASFIDKVRFLEQQNKVLETKWTLLQEQG
          GGI..VT.N..LL.PL.L..DP.IQ..RT.E.EQIKTLN.KFASFIDKVRFLEQQNK.LETKW.LLQ.Q.
Retrocopy GGITAVTVNKSLLNPLKLEVDPNIQAMRTQEKEQIKTLN-KFASFIDKVRFLEQQNKMLETKWSLLQQQ-

Parental  TKTVRQNLEPLFEQYISNLRRQLDSILGERGRLDSELRNMQDVVEDFKNKYEDEINKRTAAENEFVTLKK
          .KT.R.N....F..YI.NL.RQLD....E...L..EL.NMQ..VEDFK.KYEDEI.KRT..ENEFV..KK
Retrocopy -KTARSNMDNMFKSYINNLHRQLDTLGQEKLKLEAELGNMQGLVEDFKKKYEDEIMKRTEMENEFVIIKK

Parental  DVDAAYMNKVELQAKADSLTDEINFLRTIYDAELSQMQTHISDTSVVLSMDNNRN-LDLDSIIAEVKAQY
          DVD.AYMNKVEL......LTDEINFLR..Y..E....Q..ISD.SVVLSMDN....LD.D.IIA.V.AQY
Retrocopy DVDEAYMNKVELDSRLEGLTDEINFLRQLYEEEIRELQSQISDMSVVLSMDNSCS<LDMDGIIAQVRAQY

Parental  EEIAQRSRAEAESWYQSKYEELQVTAGRHGDDLRNTKQEIAEINRMIQRLRSEIDHVKKQCANLQSAIAD
          .EIA.RSRAE.E..Y..KYEEL...AG.H.DDLR.TK.EI.E.NR.I.RL..EI...K.Q.A.....IAD
Retrocopy KEIANRSRAEVENMYKIKYEEL*TLAGKHRDDLRRTKTEISEMNRSISRLQAEIEGLKGQRASMEAVIAD

Parental  AEQRGEMAIK--DARNKLEGLEDALQKAKQDMARLLKEYQELMNVKLALDVEIATYRKLLE
          AEQRGE.AIK..DA..KL..LE.ALQ.AKQDM.R.L.EYQEL.NVKLALD.EIATYRKLLE
Retrocopy AEQRGELAIKDADANAKLAQLEAALQQAKQDMSRQLREYQELTNVKLALDIEIATYRKLLE

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_1535 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1535 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000002190	1 retrocopy	retro_mmur_1094,
Nomascus leucogenys	ENSNLEG00000017748	2 retrocopies	retro_nleu_2823, retro_nleu_3100,
Tupaia belangeri	ENSTBEG00000000416	1 retrocopy	retro_tbel_1535 ,