RetrogeneDB ID: retro_tbel_364

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1887:104823..105655(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSIP1
• Ensembl ID: ENSTBEG00000000715
• Aliases: None
• Description: PC4 and SFRS1 interacting protein 1 [Source:HGNC Symbol;Acc:9527]

Sequence

>retro_tbel_364
GTGGATGAAGTTCCTGATGGAGCTATAAAACCACCCAAAAACAAACTACTCATTTTCTTCTTTGGAACTCATGAGACTGC
TTTCTTAGGACCAAAGGATATATTTTCTTACTCAGAAAATAAGGAAAAATATGGCAAACCAAATAAACAAAAAGGTTTTC
ATGAAGGCTTACAGGAGATAGATAACAATCCAAAAGTGAAATTTTCAAGTCAACAGGCATCTACTAAACAGTCAAACACT
TCATCTGATGTTGAAATTGAATAAAAAGAAACTAGTGTTTCAAAGGAAGATACTAATTATGAAGAAAAAAACGAGCAATG
AAGATGTAACTAAGGCAGTTGACATAACCACTCCCAAAGCTGCCAGAAGAGGGAGGAAGAGAAAAGCAGAAAAACAAGTA
GAAATCAAGGAGGCAGGAGTAGTGACAACAGCAACAGCATCTGTTAATCTAAAAGTGAGCTCTAAAAGAGGACAACCTGA
GCTACAGAGGTCAAGATTCCAAAGCCGAGGCAGACCCAAATGGTAAAGCAGCCCTGTCTTGCAGAGACCGACACGGTTAC
TGAAGAAGACCAAAATTAAGAAAAAGGGCCAAGAGGAAAAACAACCTAAAAAGCAGCTTTAAAAGTATGAAGAGGGTCAG
AGGGAAGAAGATAAACCAAGAAAAGAGCCAGGCAAAAAAGAACTGAAGAAAGAAGGTGAATCTAAAAGGAAACATTTAAC
TAAAATGGGGGTTACATCAGCCTCTGATTCTGAAGAAGAAGGAGATGATCAAGAGGGTGAAAAGAAGAGAAGAGGTGGAA
GAAACTCTCAGACTGCTCACAGAAGGGATATA

Alignment

ORF - retro_tbel_364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.41 %
• Parental protein coverage: 52.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VDEVPDGAVKPPTNKLPIFFFGTHETAFLGPKDIFPYSENKEKYGKPNKRKGFNEGLWEIDNNPKVKFSS
          VDEVPDGA.KPP.NKL.IFFFGTHETAFLGPKDIF.YSENKEKYGKPNK.KGF.EGL.EIDNNPKVKFSS
Retrocopy VDEVPDGAIKPPKNKLLIFFFGTHETAFLGPKDIFSYSENKEKYGKPNKQKGFHEGLQEIDNNPKVKFSS

Parental  QQASTKQSNTSSDVEIEEKETSASKEDTDHEE-KTSNEDVTKAIDITTPKAARRGRKRKAEKQVEIEEAG
          QQASTKQSNTSSDVEIE.KETS.SKEDT..EE.KTSNEDVTKA.DITTPKAARRGRKRKAEKQVEI.EAG
Retrocopy QQASTKQSNTSSDVEIE*KETSVSKEDTNYEE>KTSNEDVTKAVDITTPKAARRGRKRKAEKQVEIKEAG

Parental  VVTTATASVNLKVSPKRGRPA-ATEVKIPKPRGRPKMVKQPCPSETDMVTEED-KIKKKGQEEKQPKKQL
          VVTTATASVNLKVS.KRG.P..ATEVKIPKPR....MVKQPC..ETD.VTEED.KIKKKGQEEKQPKKQL
Retrocopy VVTTATASVNLKVSSKRGQPE<ATEVKIPKPR-QTQMVKQPCLAETDTVTEED>KIKKKGQEEKQPKKQL

Parental  KKDEEGQKEEDKPRKEPDKKEGKKEVESKRKNLAKTGVTSTSDSEEEGDDQEGXKKRKGGRNFQTAHRRN
          .K.EEGQ.EEDKPRKEP.KKE.KKE.ESKRK.L.K.GVTS.SDSEEEGDDQEG.KKR.GGRN.QTAHRR.
Retrocopy *KYEEGQREEDKPRKEPGKKELKKEGESKRKHLTKMGVTSASDSEEEGDDQEGEKKRRGGRNSQTAHRRD

Parental  M
          .
Retrocopy I

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_364 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_364 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012471	1 retrocopy	retro_cjac_4069,
Homo sapiens	ENSG00000164985	1 retrocopy	retro_hsap_4136,
Mus musculus	ENSMUSG00000028484	1 retrocopy	retro_mmus_2896,
Pan troglodytes	ENSPTRG00000020786	1 retrocopy	retro_ptro_2811,
Tupaia belangeri	ENSTBEG00000000715	1 retrocopy	retro_tbel_364 ,