RetrogeneDB ID: retro_tbel_4221

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_72323:1271..1811(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC90B
• Ensembl ID: ENSTBEG00000014665
• Aliases: None
• Description: coiled-coil domain containing 90B [Source:HGNC Symbol;Acc:28108]

Sequence

>retro_tbel_4221
TTCTTGACCACCACAGCCACCAAAAGATATGATGGGAGGCCAGTGGACATAACTCCTTTAGAACAAAGGAAATTAACATT
TGATACACACGCATTGGTTCAAGACTTGGAAACTCATGGATTTGACAAAACACAAGCAGAAACAATTGTATCAGCATTAG
CCACCTTATCAAATGTCTGCCTGGATACTATCTATAAAGAAATGGTCGCTCAAGCTCAGCAGAGAATAGCAGTACAACAA
TTAATGCCACATTTGGACTCCATTAGGAAAGACATGGTCATCCTAGAGAAAAGTGAATTTGCAAATCTGAGAGCGGAGAA
CGAGAAAATGAAAGTTGAACTAAACCAAGCTAAACAACAACTAATAAATGAAACAAGTCGAATTCAAGCAGATAATAAAC
TGGATATCAATTTAGAAAGGAGCAGAGTAACAGATATGGATATCCAAATCAAAAGTGTTATTTCAGAAACCAGTAACAAA
ATTGACACTGAAATTGCTTCTTTAAAAGCACTGATGGAGTCTAACAAACTTGAGACAATT

Alignment

ORF - retro_tbel_4221 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.33 %
• Parental protein coverage: 93.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLTTTAMEGYDRRPVDITPLEQRKLTFDTHALVQDLETHGFDKAQAETIVSALATLSNVSLDTIYKEMVT
          FLTTTA...YD.RPVDITPLEQRKLTFDTHALVQDLETHGFDK.QAETIVSALATLSNV.LDTIYKEMV.
Retrocopy FLTTTATKRYDGRPVDITPLEQRKLTFDTHALVQDLETHGFDKTQAETIVSALATLSNVCLDTIYKEMVA

Parental  QAQQEITVQQLMAHLDSIRKDMVILEKSEFANLRAENEKMKIELSQVKQQLINETSRIRADNKLDINLER
          QAQQ.I.VQQLM.HLDSIRKDMVILEKSEFANLRAENEKMK.EL.Q.KQQLINETSRI.ADNKLDINLER
Retrocopy QAQQRIAVQQLMPHLDSIRKDMVILEKSEFANLRAENEKMKVELNQAKQQLINETSRIQADNKLDINLER

Parental  SRVTDMD-KMPSDSKDTQTKSIISETSNKIDTEIASLKTL
          SRVTDMD....S....T..K......S.K...E...L.T.
Retrocopy SRVTDMDIQIKSVISETSNKIDTEIASLKALMESNKLETI

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_4221 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4221 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010541	2 retrocopies	retro_chof_1396, retro_chof_780,
Callithrix jacchus	ENSCJAG00000014547	1 retrocopy	retro_cjac_219,
Homo sapiens	ENSG00000137500	1 retrocopy	retro_hsap_3050,
Macaca mulatta	ENSMMUG00000020154	2 retrocopies	retro_mmul_1880, retro_mmul_773,
Nomascus leucogenys	ENSNLEG00000016478	1 retrocopy	retro_nleu_1644,
Ochotona princeps	ENSOPRG00000004144	2 retrocopies	retro_opri_197, retro_opri_682,
Pongo abelii	ENSPPYG00000003736	1 retrocopy	retro_pabe_2525,
Pan troglodytes	ENSPTRG00000004129	1 retrocopy	retro_ptro_1990,
Pteropus vampyrus	ENSPVAG00000005459	1 retrocopy	retro_pvam_614,
Rattus norvegicus	ENSRNOG00000009462	1 retrocopy	retro_rnor_868,
Tupaia belangeri	ENSTBEG00000014665	2 retrocopies	retro_tbel_3436, retro_tbel_4221 ,
Tarsius syrichta	ENSTSYG00000011196	1 retrocopy	retro_tsyr_710,
Tursiops truncatus	ENSTTRG00000003998	1 retrocopy	retro_ttru_445,
Vicugna pacos	ENSVPAG00000007753	1 retrocopy	retro_vpac_366,