RetrogeneDB ID: retro_ogar_2854

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873672.1:1138600..1139402(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF4
• Ensembl ID: ENSOGAG00000007802
• Aliases: None
• Description: PRP4 pre-mRNA processing factor 4 homolog (yeast) [Source:HGNC Symbol;Acc:17349]

Sequence

>retro_ogar_2854
TCCTCAACGGCAGCCAAACCTAAAGTGCCTGATGATTTAGTAGCTCCTGTTGGGAAGAAACTACACGTTGGTTATAGAAA
TTTGGAAGCGAAGGAGAGGGAGAGTCTGGCTCAAGTAAAGTCTGAGATTTGGGAGGAAAAAGGACTTAAAGCAGGAATCG
AAGTAGGACATACCTTTGGAGAAGTTTTTGAAACTGAGGAAAACACCAGTGAGTGCCTGGCAGAAGCGCTGGCTGAGTTT
GAAAGATGGAAGCGAAGTCAGCAAATCACTGTTTCCACAGATAACTCGGAGGTCATGACTTGCCTTAGAGCTTTGGGGGA
ACCCATCACATGTTTTGGAGAAGGCCCTGTTGAAAGAAGAGAAAGGCTTAAAAATATCCTCTCAGTAGTTGGTAGTGATG
CTTTAAAAAAGACCAAGAAGGATGATAAGAAATCTAAGAAGTCCAAAGGACTGTATGGGCAAACCTGGTACCATGAAGGA
CCAAACAGCTTGAAGGTGGCTAGACTGTGGATTGCTAAATATTCACTGCCCAGGGCAATGAAACGGTTGAACAAGGCTCC
TCTCCATAAAGAGATTCCTGAGACAACTAGAATCTCCCAGATCTAGGAGCTGCACAAATCTCTGTGCTCTTTGAATAATT
TCTACAGTCAGATTGGAGATGATCTGCCTATCTCCTCCTGTCACTTTAGTCCCAATTCCATGATGCTGGCTACAGCTTGT
TGGAGTGGGCTGTGCAAGCTCTGGTCTATTCCTGATTTCATCCCCTTTCCGCACTCGTCAAGGCCATAACACAAAAGTAG
GG

Alignment

ORF - retro_ogar_2854 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.54 %
• Parental protein coverage: 50.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSTAVKTKAPDDLVAPVVKKPHIYYGSLEEKERERLAKGESGILGKEGLKAGIEAGNINITSGEVFEIEE
          .STA.K.K.PDDLVAPV.KK.H..Y..LE.KERE.LA...S.I....GLKAGIE.G....T.GEVFE.EE
Retrocopy SSTAAKPKVPDDLVAPVGKKLHVGYRNLEAKERESLAQVKSEIWEEKGLKAGIEVGH---TFGEVFETEE

Parental  HISERQAEVLAEFERRKRARQINVSTDDSEVKACLRALGEPITLFGEGPAERRERLRNILSVVGTDALKK
          ..SE..AE.LAEFER.KR..QI.VSTD.SEV..CLRALGEPIT.FGEGP.ERRERL.NILSVVG.DALKK
Retrocopy NTSECLAEALAEFERWKRSQQITVSTDNSEVMTCLRALGEPITCFGEGPVERRERLKNILSVVGSDALKK

Parental  TKKDDEKSKKSKEEYQQTWYHEGPNSLKVARLWIANYSLPRAMKRLEEARLHKEIPETTRTSQMQELHKS
          TKKDD.KSKKSK..Y.QTWYHEGPNSLKVARLWIA.YSLPRAMKRL..A.LHKEIPETTR.SQ..ELHKS
Retrocopy TKKDDKKSKKSKGLYGQTWYHEGPNSLKVARLWIAKYSLPRAMKRLNKAPLHKEIPETTRISQI*ELHKS

Parental  LRSLNNFCSQIGDDRPISYCHFSPNSKMLATACWSGLCKLWSVPD-CNLLHTLRGHNTNVG
          L.SLNNF.SQIGDD.PIS.CHFSPNS.MLATACWSGLCKLWS.PD......T..GHNT.VG
Retrocopy LCSLNNFYSQIGDDLPISSCHFSPNSMMLATACWSGLCKLWSIPD>SSPFRTRQGHNTKVG

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_2854 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.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004571	1 retrocopy	retro_btau_1341,
Cavia porcellus	ENSCPOG00000010747	2 retrocopies	retro_cpor_1531, retro_cpor_548,
Myotis lucifugus	ENSMLUG00000015309	1 retrocopy	retro_mluc_77,
Otolemur garnettii	ENSOGAG00000007802	1 retrocopy	retro_ogar_2854 ,
Otolemur garnettii	ENSOGAG00000008960	1 retrocopy	retro_ogar_86,