RetrogeneDB ID: retro_tbel_4092

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_66933:2312..2896(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KNSTRN
• Ensembl ID: ENSTBEG00000012043
• Aliases: None
• Description: kinetochore-localized astrin/SPAG5 binding protein [Source:HGNC Symbol;Acc:30767]

Sequence

>retro_tbel_4092
GGTGGAGCGGTTGCTGCTGAGCATCTTTTGAACCAGAGCAACGAGGACTGCGGGCAGGAGCGGACCGACCTCATCATGAT
GACCAGCGGGGTTAAGACAGTGTACAGCCTGCAAACCCCCTCTATGCCTAGTGGCGGCCTGCAAACACACAAACTCGAGC
CAATTCTGAGTCTATTACCTGTTAGGACCAAAGAAGTTGATGGTCCCAGGCGTCTTCATTCAGGAGGTTCTGAGAATGCT
GTTACAAAAACAGCCAAACTAAGACAAGAGAATGGGCAGGTGAAAGCTGCAGACACAGCCAACAGGAGGAACGTGAAGAA
GAGCTACAACCATTGAGAAAGCAAAAGTCAGAGGAAGAACTCAAGGATAAGAACCAGCTCTTAGAGACTGTCAACAAACA
GTTGCACCAGAAGTTGACTGAAACTCAGGGAGAGCTGAAGGACCTGACCCAGAAAGTGGAGCTGCTGGAGAAGTTTCAGA
ACAACTGTTTGGCACTTTTGGAGAATAAGGGCCTCAATCCAGTTTTAGACAGTGAATCTCTGACATCACAGCAAGAATCC
ACTATGGATCACACAAGCTCTATG

Alignment

ORF - retro_tbel_4092 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.66 %
• Parental protein coverage: 64.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGAVAAEHLLNQSKEDCGRERWAPGADLITMTSVVKTVYSLQTPSVPSGGLPADTQTRANSKSLLPVRTK
          GGAVAAEHLLNQS.EDCG.ER.....DLI.MTS.VKTVYSLQTPS.PSGGL...T.......SLLPVRTK
Retrocopy GGAVAAEHLLNQSNEDCGQER----TDLIMMTSGVKTVYSLQTPSMPSGGL--QTHKLEPILSLLPVRTK

Parental  EVDVPRHFHSGGSENDVTKTAKPRQENGQAKAADTANRRNVKKSY-KPLRKQKSEEELKDKNQLLEAVNK
          EVD.PR..HSGGSEN.VTKTAK.RQENGQ.KAADTANRRNVKKSY..PLRKQKSEEELKDKNQLLE.VNK
Retrocopy EVDGPRRLHSGGSENAVTKTAKLRQENGQVKAADTANRRNVKKSY<QPLRKQKSEEELKDKNQLLETVNK

Parental  QLHQKLTETQGELKDLTQKVELLEKFQNNCLALLESKGLNPVLGSESLTSQQESTTDHTGSM
          QLHQKLTETQGELKDLTQKVELLEKFQNNCLALLE.KGLNPVL.SESLTSQQEST.DHT.SM
Retrocopy QLHQKLTETQGELKDLTQKVELLEKFQNNCLALLENKGLNPVLDSESLTSQQESTMDHTSSM

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_4092 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4092 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000032340	2 retrocopies	retro_btau_1217, retro_btau_274,
Choloepus hoffmanni	ENSCHOG00000007085	3 retrocopies	retro_chof_1378, retro_chof_2237, retro_chof_504,
Monodelphis domestica	ENSMODG00000000464	1 retrocopy	retro_mdom_1200,
Otolemur garnettii	ENSOGAG00000009825	1 retrocopy	retro_ogar_1829,
Tupaia belangeri	ENSTBEG00000012043	4 retrocopies	retro_tbel_2696, retro_tbel_3958, retro_tbel_4092 , retro_tbel_787,
Tursiops truncatus	ENSTTRG00000010577	1 retrocopy	retro_ttru_240,