RetrogeneDB ID: retro_tbel_3958

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_448:22963..23552(-)
• 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_3958
GGAGTGGATGTCGCTGAGCATCTTTTGAACCCGGAGCAATGAGGACTGAGGGCAGGAGCAGACCCACCTCATCACGATGA
CCAGCGTGGTTAAGACAGTGTACAACCCGCAAATCCCCTCTGTGCCAAACAGCGGCCTGCCTGCAGACACACGAACTCGA
GCCAATTCTAAGAGTCTATTACCTGTCAGGACCAAGGAAGTCAATGTTCCCAAGTATTTTCATTCAGGAGGCTCTGAGAA
TGATGTTACAAAAACAGCCAAACCAAGACAAGAGAATGGGCAGGTGAAAGCTGCAGAAACAGCCAACAGGAGAAATGTGA
AGAAGAGCTACAAACCATTGAGAAAGCAAAAGTCAGAGGAAGAACTCAAGGATAAGAATGAGCTCTTTGAGGCTGTCAAC
AAGCATTTGTACCAGAAGTTGACTGAAACTCAGGGAGAGCTGAAGGACCTGACCCAGAAAGTGGAGCTGCTGGAGAAGTT
TCAGAACAACTGTTTGGCAATTTTGGACAGTAAGGGCCTCAACCCAGTTTTAGGCAGTGAATCTCAGACATCACAGCAAG
AATCCACTATGGATCACACAAGTTCTATG

Alignment

ORF - retro_tbel_3958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.59 %
• Parental protein coverage: 63.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAVAAEHLLN-QSKEDCGRERWAPGADLITMTSVVKTVYSLQTPSVPSGGLPADTQTRANSKSLLPVRTK
          G...AEHLLN..S.ED.G.E.......LITMTSVVKTVY..Q.PSVP..GLPADT.TRANSKSLLPVRTK
Retrocopy GVDVAEHLLN>RSNED*GQEQ----THLITMTSVVKTVYNPQIPSVPNSGLPADTRTRANSKSLLPVRTK

Parental  EVDVPRHFHSGGSENDVTKTAKPRQENGQAKAADTANRRNVKKSYKPLRKQKSEEELKDKNQLLEAVNKQ
          EV.VP..FHSGGSENDVTKTAKPRQENGQ.KAA.TANRRNVKKSYKPLRKQKSEEELKDKN.L.EAVNK.
Retrocopy EVNVPKYFHSGGSENDVTKTAKPRQENGQVKAAETANRRNVKKSYKPLRKQKSEEELKDKNELFEAVNKH

Parental  LHQKLTETQGELKDLTQKVELLEKFQNNCLALLESKGLNPVLGSESLTSQQESTTDHTGSM
          L.QKLTETQGELKDLTQKVELLEKFQNNCLA.L.SKGLNPVLGSES.TSQQEST.DHT.SM
Retrocopy LYQKLTETQGELKDLTQKVELLEKFQNNCLAILDSKGLNPVLGSESQTSQQESTMDHTSSM

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_3958 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3958 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,