RetrogeneDB ID: retro_tbel_2369

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_109598:945..1601(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000015631
• Aliases: None
• Description: None

Sequence

>retro_tbel_2369
CAACTCCTCCATCTCCAACTCTTTCTAATCTGTGTCCTTTGTGGAGGGTCCTTCATCGATGCCACAACCACAATAGAATG
TCTACATTCCTTCTGTAAAACATGCACCATGTGTTACCTGGAGAACAGCAAGTATTGTCTTATCTGTGATGTCCAAGTTC
ACAAAACCAGACCACTACTTAATACAAGGTCAGATAGAACTCTTCAAGATATTGTATACGAATTAGTTCCAGGGCTCTTC
GAAATTGAAATGAAGAAAAGAAAGGATTATTTTTATGCAGTTCACCCTTCAGCTGATGCTGCCAATGGCTCTAATTAAGG
CATAGAAGTTGCAGTTGAAGATAAGAGAATTATAACTGATAATGAGATAATAAGCTTATCCATTGAATTTTTAAAACAGA
ACAAACTGGATTGGAAAGTAAACAAAGACAAAGAGAAATCTAAGGAGGAGGTGAATGATAAAACATATGTATGATGCCCA
GCAGGAATGAGTATGATGGACTTAAGAAAGTTTCTCAGAAGCAAAATGGACATACCTAATACTTTCCAGATTGATGTCAT
GAATGAAGAAGAACCTATATCCATTACTATATGTAAATGGATATTGCTTACATATATACCTGAAGAAGGAATGGTCCTCT
TCTTTTGAAATACAGA

Alignment

ORF - retro_tbel_2369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.66 %
• Parental protein coverage: 67.18 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKTLQD
          ....L...L.CVLCGG.FIDATT.IECLHSFCKTC...YLE.SKYC.ICDVQVHKTRPLLN.RSD.TLQD
Retrocopy QLLHLQLFLICVLCGGSFIDATTTIECLHSFCKTCTMCYLENSKYCLICDVQVHKTRPLLNTRSDRTLQD

Parental  IVYKLVPGLFKNEMKRRRD-FYAAHPSADAANGSNEDRGEVADEDKRIITDDEIISLSIEFFDQNRLDRK
          IVY.LVPGLF..EMK.R.D.FYA.HPSAD.A........EVA.EDKRIITD.EIISLSIEF..QN.LD.K
Retrocopy IVYELVPGLFEIEMKKRKDYFYAVHPSAD-AANGSN*GIEVAVEDKRIITDNEIISLSIEFLKQNKLDWK

Parental  VNKDKDKSKEEVNDKRYLRCPAAMTVMHLRKFLRSKMDIPNTFQIDVMYEEEPLK-DYYTLMDIAYIYTW
          VNKDK.KSKEEVNDK.Y..CPA.M..M.LRKFLRSKMDIPNTFQIDVM.EEEP....YY..MDIAYIYT.
Retrocopy VNKDKEKSKEEVNDKTYV*CPAGMSMMDLRKFLRSKMDIPNTFQIDVMNEEEPIS<HYYM*MDIAYIYT*

Parental  RRNGPLPLKYR
          RRNGPL.LKYR
Retrocopy RRNGPLLLKYR

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_2369 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2369 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011962	1 retrocopy	retro_chof_709,
Callithrix jacchus	ENSCJAG00000036548	1 retrocopy	retro_cjac_2437,
Cavia porcellus	ENSCPOG00000015427	2 retrocopies	retro_cpor_1209, retro_cpor_546,
Gorilla gorilla	ENSGGOG00000025243	1 retrocopy	retro_ggor_3025,
Loxodonta africana	ENSLAFG00000016845	1 retrocopy	retro_lafr_591,
Macaca mulatta	ENSMMUG00000000881	1 retrocopy	retro_mmul_2591,
Mus musculus	ENSMUSG00000026739	1 retrocopy	retro_mmus_3710,
Oryctolagus cuniculus	ENSOCUG00000005420	1 retrocopy	retro_ocun_489,
Tupaia belangeri	ENSTBEG00000015631	1 retrocopy	retro_tbel_2369 ,