RetrogeneDB ID: retro_tbel_1428

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4684:56791..58096(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSP90AB1
• Ensembl ID: ENSTBEG00000014873
• Aliases: None
• Description: heat shock protein 90kDa alpha (cytosolic), class B member 1 [Source:HGNC Symbol;Acc:5258]

Sequence

>retro_tbel_1428
AAGTACATTGATCAAGAAGAACTCAACAAAACCAAACCTATTTGGACCAGAAATCCTGATGATATTACTAATGAAGAGTA
TGGAGAATTCTACAAGAGCTTGACCAATGACTGGGAAGATCACTTGGCAGTGAAGCACTTTTCAGTCGAAGGACAGCTGG
AATTCAGAGCTCTTTTTTTCGTTCCAAGACGTGCTCCTTTTGACTTGTTTGAAAACAGGAAGAAAAAGAACAACATTAAG
TTGTATGTACGCAGAGTATTCATCATGGACAATTGTGAAGAGCTGATCACTGAATGTCTGAATTTCATTAGAGGAGTAGT
GGACTCTGAGGATCTCCCTCTAAATATTTCCCATGAGATGTTGCAGCAAAGTAAAATTCTGAAAGTTATCAGAAAGAATT
TGGTCAAAAAATGCTTAGAACTTTTCACCGAATTGGCGGAAGATAAAGAGAACTGCAAGAAGTTCTATGAGCAGTTTTCT
AAAAATATAAAGCTTGGAATTCATGAAGACTCTCAAAATCGTAAGAAACTTTCAGAGTTGTTAAGGTATTACACGTCTGC
TTCTGGTGATGAGATGGTATCCCTGAAGGGTTATTGCACCAGAATGAAGGAAAACCAGAAGCATATCTATTATATCACAG
GTGAGCCCAAGGACCAGGTAGCTAATTCGGCCTTCATAGAACGTCTTCGGAAAGCACGGCTTAGAAGTGATCTATATGAT
TGACCTATCGATGAGTACTGTGTCCAACAGCTGAAGGAATTTGAGGGGAAGACTTTAGTGTCAGTCACCAAAGAGGGTCT
AGAACTTCCAGAAGATGAAGAAGAGAAAAAGAAACAGGAAGAGAAAAAAACAAAGTTTGAAAACCTTTGCAAAATCATGA
AAGATATCTTGGAGAAAAGAGTGGAGAAGGTAGTTGTCTCAAACCGGTTGGTAATGTCCCCATGCTGCATCATCACAAGC
ACATACGGCTGGACAGCAAACATGGAGAGAATCATGAAAGCGCAAGCCTTAACAGACAACTCCACAATGGGTTACCGGGC
TGCCAAGAAGCACCTGGAGATCAACCCTGATCATTCCATCATTGAGACCTTAAGGCAAAAGGCAGAGGCTGACAAGAACA
ACAAGTCTGTGAAGGATTTGGTCATCTTGCTTGATGAAACCACACTCCTGTCTTCTGGGTTTAGTCTGGAAGATCCCCAG
ACACATGCTAACAGAATCTACAGGATGATCAAACTTGGTCTGGGTATTGATGAAGATGACCCTACTGCTGATGATACCAG
TGCTGCTGTGACTGAAGAAATGCCA

Alignment

ORF - retro_tbel_1428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.32 %
• Parental protein coverage: 60. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLF
          KYIDQEELNKTKPIWTRNPDDIT.EEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRAL.F.PRRAPFDLF
Retrocopy KYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALFFVPRRAPFDLF

Parental  ENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLE
          EN.KKKNNIKLYVRRVFIMD.C.ELI.E.LNFIRGVVDSEDLPLNIS.EMLQQSKILKVIRKN.VKKCLE
Retrocopy ENRKKKNNIKLYVRRVFIMDNCEELITECLNFIRGVVDSEDLPLNISHEMLQQSKILKVIRKNLVKKCLE

Parental  LFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIY
          LF.ELAEDKEN.KKFYE.FSKN.KLGIHEDS.NR..LSELLRY.TS.SGDEM.SL..Y..RMKE.QK.IY
Retrocopy LFTELAEDKENCKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKGYCTRMKENQKHIY

Parental  YITGESKEQVANSAFVERVR-KRGFEVVYMTE-PIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKK
          YITGE.K.QVANSAF.ER.R.K.G.EV.YM...PIDEYCVQQLKEF.GK.LVSVTKEGLEL.........
Retrocopy YITGEPKDQVANSAFIERLR>KHGLEVIYMID<PIDEYCVQQLKEFEGKTLVSVTKEGLELXXXXXXXXX

Parental  MEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMA
          ...........CK.MK.IL.K.VEKV..SNRLV.SPCCI.TSTYGWTANMERIMKAQAL.DNSTMGY..A
Retrocopy XXXXXXXXXXXCKIMKDILEKRVEKVVVSNRLVMSPCCIITSTYGWTANMERIMKAQALTDNSTMGYRAA

Parental  KKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDE
          KKHLEINPDH.I.ETLRQKAEADKN.K.VKDLV.LL.ET.LLSSGFSLEDPQTH.NRIYRMIKLGLGIDE
Retrocopy KKHLEINPDHSIIETLRQKAEADKNNKSVKDLVILLDETTLLSSGFSLEDPQTHANRIYRMIKLGLGIDE

Parental  DEVTAEEPSAAVPDEIP
          D..TA...SAAV..E.P
Retrocopy DDPTADDTSAAVTEEMP

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_1428 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1428 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 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001981	4 retrocopies	retro_cfam_1108, retro_cfam_411, retro_cfam_562, retro_cfam_881,
Felis catus	ENSFCAG00000009764	1 retrocopy	retro_fcat_1177,
Gorilla gorilla	ENSGGOG00000008889	2 retrocopies	retro_ggor_1011, retro_ggor_701,
Macropus eugenii	ENSMEUG00000013735	1 retrocopy	retro_meug_1896,
Myotis lucifugus	ENSMLUG00000005239	2 retrocopies	retro_mluc_1604, retro_mluc_865,
Mus musculus	ENSMUSG00000023944	3 retrocopies	retro_mmus_1916, retro_mmus_3528, retro_mmus_856,
Otolemur garnettii	ENSOGAG00000011961	1 retrocopy	retro_ogar_2574,
Pongo abelii	ENSPPYG00000016655	2 retrocopies	retro_pabe_2425, retro_pabe_415,
Pan troglodytes	ENSPTRG00000018217	4 retrocopies	retro_ptro_1850, retro_ptro_1968, retro_ptro_2003, retro_ptro_880,
Tupaia belangeri	ENSTBEG00000014873	1 retrocopy	retro_tbel_1428 ,