RetrogeneDB ID: retro_ogar_887

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873530.1:8622461..8623045(+)
• Located in intron of: ENSOGAG00000031795

Retrocopy information

• Ensembl ID: ENSOGAG00000024162
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAD51D
• Ensembl ID: ENSOGAG00000009880
• Aliases: None
• Description: RAD51 paralog D [Source:HGNC Symbol;Acc:9823]

Sequence

>retro_ogar_887
ATGGGCATACTCAGGGTCAGACTGTGCCCAGGCCTCGCCCAGAAGATTGTCCACCTTCTGAGGAGTTGCAGGATCAAGAC
AGTAGTGGACCTGGTTTCTGCAGACCTGGAGGTGGTAGCTCAGAAATGTGGCTTGTCTTATAAGGCCCTGGTTGCCTTGA
TGCAGGTGCCGCTGGTTCAGTTCTCAGCTTTCCCCTTCAATGGTGCTGATCTCTATGAAGAACTAAAGACTCCACTGTCA
TCCTGTCTACTAGCATAGGCAGCCTGGACAAATTACCTGACCCTGGTTTCTCTCCTGGAGAAGTGACTGAAATTATAGGA
GGCCCAGATAGTGGCAAAACTCAGTTATGTCTTTGTGTGGCATCAAACATAGCCCATGGCCTGTAGCAAAATGTCCTGTA
TGTTGATTCCAAAGGAGGGATGACAGCCTCTTGCCTCCTATAGTTACTTGAGGCTAGGATCCAGGATGAAGAGGAACAGG
TAAGAGCTCTCCAGAGGATCCGGGTGGCACATGCATTTGACATCTTCCAGATGTTGAATGTGCTGAAGGATCTCTGAGGC
ACTGTGGCCCAACAGGTGAACAAT

Alignment

ORF - retro_ogar_887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 59.45 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGVLRVGLCPGLTQEMVHLLRSRGIKTVVDLVSANLEEVAQKCGLSYKALVALRRVLLAQFSAFPINGAD
          MG.LRV.LCPGL.Q..VHLLRS..IKTVVDLVSA.LE.VAQKCGLSYKALVAL..V.L.QFSAFP.NGAD
Retrocopy MGILRVRLCPGLAQKIVHLLRSCRIKTVVDLVSADLEVVAQKCGLSYKALVALMQVPLVQFSAFPFNGAD

Parental  LYEELKT-STAILSTGIASLDKLLDTGLYTGEVTEIVGGPGSGKTQICLCVAANVAHGLQQNVLYIDSNG
          LYEELKT.ST.ILST.I.SLDKL.D.G...GEVTEI.GGP.SGKTQ.CLCVA.N.AHGL.QNVLY.DS.G
Retrocopy LYEELKT<STVILSTSIGSLDKLPDPGFSPGEVTEIIGGPDSGKTQLCLCVASNIAHGL*QNVLYVDSKG

Parental  GLTASRLLQLLEARTQDEEEQARALQRIQVAHAFDIFQMLNVLQDLRSTVAQQVTS
          G.TAS.LL.LLEAR.QDEEEQ.RALQRI.VAHAFDIFQMLNVL.DL..TVAQQV..
Retrocopy GMTASCLL*LLEARIQDEEEQVRALQRIRVAHAFDIFQMLNVLKDL*GTVAQQVNN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_887 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019082	1 retrocopy	retro_btau_1859,
Otolemur garnettii	ENSOGAG00000009880	1 retrocopy	retro_ogar_887 ,