RetrogeneDB ID: retro_ogar_1907

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873573.1:5306539..5308031(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEPDC1
• Ensembl ID: ENSOGAG00000000934
• Aliases: None
• Description: DEP domain containing 1 [Source:HGNC Symbol;Acc:22949]

Sequence

>retro_ogar_1907
TTTGCTACAACTTCCCCTCTTAAAACTCTCCCACGAAGACATCCGGAATTGAGAAAAGCATCATAGACAACTTTCCTAAA
GATACAGATAGTATTTTTAAATTACAAAACTTATAGAATTCCTAAAAAGCATGGATCACATTTCTGTTAGGAAAATAAAG
AGATACAGTATGAAATAATTAATGAAGATCAAGAACATTTAGTTGATAATAAAGCAATAAGCCAGGTAGATGTTGAAGAA
GTTTGGAGATCTATTATTCTGATCTACCTGCAGAGCATTTTAGGTGTGCCATCTCTAGAAGAATTCATAAATCCAAGATG
AGTAATTCCTCAGTGTGTGGTGTACCATGTGGCCAGTACAAGTGGATGTGGACTGGTTATATTGCAAGACGAAGCAGGGA
ACCCTCCTCCCTGGGTATTTATTTGCCATGAAGTGCCTACAAATTGGCCAAGAAGCAATGCCGTGGGTAATCCCGCCTAT
GTTGGCTTTGAAGAAGATGTATTTAGAACAATTGCAAATTATTTTCTAGATTTCTCTGAACCCTTCTTACCTTTGGATAT
TATGAATTATTTGTTAACATTTTGGTTGTCTGTGGCTACATCACAGTTTCAGACAGACCCAGTGGAATACATACAATCTA
AGACCATCCACAATCTTCAAAAACCCTTCACTTAAACACTTTGAATTCCTTCAGATCAACTGAGTGTTGTCTTCTCAGTC
TGCTTCAGAAAGACAGAAACTCAGAGGAATCAGATTCTACTGAGAGACTACAGGTAAGTGGTCAAGGATTTCAAGAAAGA
TGTGCTAAGAAAATGCAGCTAGTTAATTTAGAAGGCAGAAGAGTGAGAGCTAATGACATCGTGGGCGAAGTTGTCACAAT
TTAATGGGCTTCCGTAGCGTGTGTGTTCTGTCCTGTAATGTCAAACCGAGGTACTGTTCTTTGGAAGGAATCGTAGATGT
GCCAGGGAGTTCAAGGAAAGAGAGGTCCAGCGTCTGCCATCAATCTGTTCAGAACATAGAAGGACAAAATAATAAACATT
TTTTAGGATTTAAGCCCAAGCGAGAAATCCAATTTGATTGTCGTTCAGAGGAAAGTATTCAAAAGCCATTCAGCGCTGGC
TTTAAGAGAAGCTCTCCCCTGGCTGTCCAAGACCAAGAGGACGAGTTACATAGTAGGAAATGCGAGTCAGAGCTGCTTTG
TAGGCCCCAGAGTTTGCTTTTGAGAAGCAGTACAAGAAGGAATAGTTATGTCAATACGCCAGTGGCCGAAATTATCATGA
AACCAAATCTTAGACAAGGCAGCCCAGGGTACAAACCACTGTGGAAAGTGAACTTGGAGAGTCTAGTATCACAGTCAACT
AAACACGCTGCAAAAGCACAATAGAACTCACAGAAAATTCTACCTCCAGCTTCTTTTGTGTTGACTCGAGTCCAAAGTTT
GCTGAAACCTCACTTAGAAAGGGTCTCCATCGACGCCTGGCAGCTATGCTGT

Alignment

ORF - retro_ogar_1907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 61.78 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  FPTTSPLKALPRRHPELRKSS-IDNFPKDKDS-IFKLRNLSRRTPKKHGLHFSQENIEKIKHEIINEDQE
          F.TTSPLK.LPRRHPELRK.S.IDNFP..KD..I..L.....R.PKKHG.HF..EN.E.I..EIINEDQE
Retrocopy FATTSPLKTLPRRHPELRKAS<IDNFP--KDT>IVFLNYKTYRIPKKHGSHFC*ENKE-IQYEIINEDQE

Parental  NLVDNREISQEDIKEVWRYVILTHLQTILGVPSLEEFINPRQIIPQYVMYNVANTSRRGVVLLQDKADDL
          .LVDN..ISQ.D..EVWR..IL..LQ.ILGVPSLEEFINPR..IPQ.V.Y.VA.TS..G.V.LQD.A...
Retrocopy HLVDNKAISQVDVEEVWRSIILIYLQSILGVPSLEEFINPR*VIPQCVVYHVASTSGCGLVILQDEAGNP

Parental  PHWV-LSAMKCL-ANWPRSNDVNNPTYVGFERDVFRTIADYFLDLPEP-LLTFEYYELFVNILVVCGYIT
          P.WV.L.AMKCL..NWPRSN.V.NP.YVGFE.DVFRTIA.YFLD..EP.LLTF.YYELFVNILVVCGYIT
Retrocopy PPWV>LFAMKCL<TNWPRSNAVGNPAYVGFEEDVFRTIANYFLDFSEP<LLTFGYYELFVNILVVCGYIT

Parental  VSDRPSGTHKIQDHPQSSETLHINSLNSFKSTECLLLSLLRKDKTKEESDSTERLQTSGQGFQESCAGNM
          VSDRPSG.H.I.DHPQSS.TLH.N.LNSF.STEC.LLSLL.KD...EESDSTERLQ.SGQGFQE.CA..M
Retrocopy VSDRPSGIHTI*DHPQSSKTLHLNTLNSFRSTECCLLSLLQKDRNSEESDSTERLQVSGQGFQERCAKKM

Parental  QLVNLKSRRVSANDIV-GGSCQNLMGFHSGRALSSSIKPRCCSLEGIVDVPGSSRKETSSVFHQSVLNIE
          QLVNL..RRV.ANDIV.G.SC.NLMGF.S...LS...KPR.CSLEGIVDVPGSSRKE.SSV.HQSV.NIE
Retrocopy QLVNLEGRRVRANDIV<GRSCHNLMGFRSVCVLSCNVKPRYCSLEGIVDVPGSSRKERSSVCHQSVQNIE

Parental  GQNYKHFLESKPKQEFQSSLHSEESIQKPLSAGFKRSSALTVQDQE-ELLTRKCKSKQLCRSQSLLLRSS
          GQN.KHFL..KPK.E.Q....SEESIQKP.SAGFKRSS.L.VQDQE.EL..RKC.S..LCR.QSLLLRSS
Retrocopy GQNNKHFLGFKPKREIQFDCRSEESIQKPFSAGFKRSSPLAVQDQEDELHSRKCESELLCRPQSLLLRSS

Parental  SRRNSYINTPVAEIIMKPNLGQGS-TRVQTATESELGESSITVTKRLCRSTIELTENPS-PAAASVLTGT
          .RRNSY.NTPVAEIIMKPNL.QGS..RVQT..ESELGESSITV....C.STIELTEN...PA...VLT..
Retrocopy TRRNSYVNTPVAEIIMKPNLRQGS<PRVQTTVESELGESSITVN*TRCKSTIELTENST>PA-SFVLTRV

Parental  QSLLKPHLERVAIDALQLCC
          QSLLKPHLERV.IDA.QLCC
Retrocopy QSLLKPHLERVSIDAWQLCC

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_1907 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013839	1 retrocopy	retro_cpor_735,
Homo sapiens	ENSG00000024526	2 retrocopies	retro_hsap_1545, retro_hsap_4206,
Gorilla gorilla	ENSGGOG00000016316	1 retrocopy	retro_ggor_1176,
Macaca mulatta	ENSMMUG00000017766	1 retrocopy	retro_mmul_1176,
Mus musculus	ENSMUSG00000028175	1 retrocopy	retro_mmus_3028,
Nomascus leucogenys	ENSNLEG00000009334	1 retrocopy	retro_nleu_2931,
Otolemur garnettii	ENSOGAG00000000934	1 retrocopy	retro_ogar_1907 ,
Pongo abelii	ENSPPYG00000001248	1 retrocopy	retro_pabe_3441,
Pan troglodytes	ENSPTRG00000000847	2 retrocopies	retro_ptro_1041, retro_ptro_2855,