RetrogeneDB ID: retro_tbel_4671

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_97483:49879..50576(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD51AP1
• Ensembl ID: ENSTBEG00000010089
• Aliases: None
• Description: RAD51 associated protein 1 [Source:HGNC Symbol;Acc:16956]

Sequence

>retro_tbel_4671
CTGAAAGAAAACATCATACCACAAGAAAAAGCACCTAAAAAAAGGGTAGCTTTAGATGACAAGTTCTACCAGAGAGACTT
AGAAGTCGCACTGGTTTTTATCAGTGAAGGAACTCCCCACAGTCACTGCTGATGTGCAGAAATCTCAAGATGAAAGCATT
GAAAAACATGGCAATAGTGAGACAAAAACGATGAATAAATCTGTTTGTATCTCTAACTGCAGTGTAGCCAGTGATCAGTT
AGATTTGGATACGATTACTGAGGAGGAGGATAGTTATGGTGTTCAGAGGAAAAGAAAAACAGCATCCAAAACTGTGGTCC
AACAGAGGAAGATTCTTTTGGAAAGCAGTGATGCCAATAGTCCTGATGACTCTGAACCAGACTTTGTAACTGGTGAGGAT
TCCAAGGATGATTCTGATTTTGGTGAGAGTGAAGATGATGTCGAAGACCTCACTGTGAGAAAAAGCAAAGTTAAAGAAAT
TAAAAAGAGAGAAGTGAAGGTAAAACTCCCAGTAGACAAGAAAAAAAAGAAATCTCAATCTAGACGTAATACTTTGGTGG
ACTCTGCTCCTGATGTAATCAGATCAGAATCTCAGTCTTCACCAAAAAAGGCTTCTCTTTTTTCAGAGGCCACCGGGAAG
CCATTACAAATGTGCAGCCCTCCAGCTGAGAGTAAGAGACCTAAGTGGGTCCCACCA

Alignment

ORF - retro_tbel_4671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.15 %
• Parental protein coverage: 78.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LEDTFTASAHAVSHTVSLDDKLYQRDLEVALA-LSVKEPPTATVDVQKSQDESIEKHGSGETETMSKSVR
          L.........A....V.LDDK.YQRDLEVAL..LSVKE.PT.T.DVQKSQDESIEKHG..ET.TM.KSV.
Retrocopy LKENIIPQEKAPKKRVALDDKFYQRDLEVALV>LSVKELPTVTADVQKSQDESIEKHGNSETKTMNKSVC

Parental  ISNCSVASDHLDLDKISEEEDIHDVHRKRKAASKAVVQQRKILLEGSDADSPDDSEPDFATGEDSEDDSD
          ISNCSVASD.LDLD.I.EEED...V.RKRK.ASK.VVQQRKILLE.SDA.SPDDSEPDF.TGEDS.DDSD
Retrocopy ISNCSVASDQLDLDTITEEEDSYGVQRKRKTASKTVVQQRKILLESSDANSPDDSEPDFVTGEDSKDDSD

Parental  FGESEDDDEDLTMRKSKVKEIKEIKKREVKVKPPVDKKEKKSQSRRNTLVTSVDSAPDAIRPQSQSSPKK
          FGESEDD.EDLT.RKSKVKEIK...KREVKVK.PVDK...KSQSRRNTLV...DSAPD.IR..SQSSPKK
Retrocopy FGESEDDVEDLTVRKSKVKEIK---KREVKVKLPVDKXXXKSQSRRNTLV---DSAPDVIRSESQSSPKK

Parental  APLSSEATRKPLQLCSPPAESKRPKWVPP
          A.L.SEAT.KPLQ.CSPPAESKRPKWVPP
Retrocopy ASLFSEATGKPLQMCSPPAESKRPKWVPP

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_4671 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4671 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
Choloepus hoffmanni	ENSCHOG00000010098	1 retrocopy	retro_chof_2173,
Homo sapiens	ENSG00000111247	1 retrocopy	retro_hsap_2841,
Nomascus leucogenys	ENSNLEG00000003178	1 retrocopy	retro_nleu_1595,
Tupaia belangeri	ENSTBEG00000010089	1 retrocopy	retro_tbel_4671 ,