RetrogeneDB ID: retro_tbel_1610

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5237:51153..51863(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD11
• Ensembl ID: ENSTBEG00000001962
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 11 [Source:HGNC Symbol;Acc:9556]

Sequence

>retro_tbel_1610
GCAGCTCATCTGGTCCCATCCCTTCTTGATCTGTTTCTTTATATGGAAGCAGCTACAGAGCAGCAGGTTGAACTGTGTTT
AGAATGTACTGAATGGGCCAAGTCAGAGAAAAGAACTCTTTTACACCAAGCTTTGGAGGCAAGTCTGGTGTCTTTGTTCT
TTGCTACCAAGAGGTACCAGGAAGCATTACATTCGGGTTCTCAGCTGCTGGGAGAGTTGTAAAAGATGGATGACAAAGTC
CTTTTGGTGGAAGTACAACTTTTGGAAAGCAAAACATACCACGCTTTGAGCAACCTTCAGAAAGCCTGAATTGCTTTAAC
CTCTGCTAGAACCACAGCAAACGCCATCGACTACCCCCCTAATTGCAGGCCACCTTGCGCATGCAGTCAGGTATTATCCA
CGCAGCTGAGGGGCAGGACTGGAAAACTGCAACTCATATTTCTATGAGGCAAATATTTGAGGGTTATGACTCCCCTGAAA
ACCCTAAGGCCATCACATCTCTGAAGTACATGTTGCTGTGCAAAATTATGCTCAACACCCCAGAAGATGTCCAGGCTTTG
GTAAGCAGGAAGCTTGCACTTCGGTATGCAAGGAGGCAGACAGAGGCATTAAACTGTGTAGCACAGGCTACCAAGAAGAG
ATCACTGGCAGATTTTGAAAAGGCCCTGACAGATTACTGGGCAGAGCTCCGGGAGAACCCCATCATTGCG

Alignment

ORF - retro_tbel_1610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.09 %
• Parental protein coverage: 55.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AARLVRSLLDLFLDMEAATGQEGELCLECIEWAKSEKRTFLRQALEARLVSLYFDTKRYQEALHLGSQLL
          AA.LV.SLLDLFL.MEAAT.Q..ELCLEC.EWAKSEKRT.L.QALEA.LVSL.F.TKRYQEALH.GSQLL
Retrocopy AAHLVPSLLDLFLYMEAATEQQVELCLECTEWAKSEKRTLLHQALEASLVSLFFATKRYQEALHSGSQLL

Parental  RELKKMDDKALLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPK-LQATLDMQSGIIHAAEEK
          .EL.KMDDK.LLVEVQLLESKTYHALSNL.KA..ALTSARTTANAI..PP..LQATL.MQSGIIHAAE..
Retrocopy GEL*KMDDKVLLVEVQLLESKTYHALSNLQKA*IALTSARTTANAIDYPPN<LQATLRMQSGIIHAAEGQ

Parental  DWKTA-YSYFYEAFEGYDSIDSPKAITSLKYMLLCKIMLNTPEDVQALVSGKLALRYAGRQTEALKCVAQ
          DWKTA........FEGYDS...PKAITSLKYMLLCKIMLNTPEDVQALVS.KLALRYA.RQTEAL.CVAQ
Retrocopy DWKTATHISMRQIFEGYDSPENPKAITSLKYMLLCKIMLNTPEDVQALVSRKLALRYARRQTEALNCVAQ

Parental  ASKNRSLADFEKALTDYRAELREDPIIS
          A.K.RSLADFEKALTDY.AELRE.PII.
Retrocopy ATKKRSLADFEKALTDYWAELRENPIIA

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_1610 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1610 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014450	1 retrocopy	retro_cjac_4166,
Mus musculus	ENSMUSG00000017428	1 retrocopy	retro_mmus_1973,
Tupaia belangeri	ENSTBEG00000001962	1 retrocopy	retro_tbel_1610 ,
Tupaia belangeri	ENSTBEG00000008306	1 retrocopy	retro_tbel_4497,