RetrogeneDB ID: retro_ogar_1417

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873546.1:11357662..11358752(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NCL
• Ensembl ID: ENSOGAG00000027852
• Aliases: None
• Description: nucleolin [Source:HGNC Symbol;Acc:7667]

Sequence

>retro_ogar_1417
GTCAGAATTGGTATGACTAGAAAGTTTGGCTATGTGGATTTTGACTCTGTGGAAGACCTGGAAAAGCCTTGCAGCTCACT
GGTTTGAAAGTCTTTGGCAATGAAATTGAACTAGAGAAACCAAAAGGGAAAGACAGTAAGAAAGAGCGAGATACAAGAAC
ACTTTTGGCCCAAAACCTTCCTTCCAAAGTCACTCAGGATGAATTAAAAGAAGTGTTTGAAGGTGCTATGGAGATCAGAA
TAGTCAGCAAGAATGGGAAGAGTACAGGGATTGCTAATATTGAATTTAAGACAGAAGCTGATGCAGAGAAAACATTTGAA
GAAAAGCAGGGAACAGAGATTGCCTGGTGATCCATTTCCCTGTACTATACTGGGGAGAAAGGTCAAAGTCAAGACTATGG
GGGTGGAAAGAATAGTACTTGGAGCTATGAATCAAAAACTCTGGTTTTAAGCAAACTGTCCTACAGTGCAACAGAAGAAA
CTCTTCAGGAAGTGTTTGAGAAGGCATCTTTTATCAAAGCGCCCCCGAACCAAATGGGCAAATCCAAAGGGTATGCATTT
ATAGAATTTGCTTCATTTGAAGATACTAAAGAAGCTTTAAATTCCTGTAATAAGAGGGAAATTGAGGGAGAGCAATCAGG
CTGGAGTTAGAAGCACCCAGAGGATCACCTAATGCCTGAAGCCAACCATCCAAAGCTCTGTTTGTCAAAGGTCTGTCTGA
GGACACCACTGGAGAGACATTGAAGGAGTCATTTGACAGCTCTGTTCACGCACAGATAGTCACTGACAGGGAACCTGGGT
CTTCCAAAGGCTTTGAGTTTCTAAACTTCAACAGTGAGGAAGATGCCAAAGCTGCAAAGGAGGCCATGGAAAATGGTGAA
ACTGATGGAAACAAAGTTACCTTGGACTGGGTCAAGCCTAAGGATGAAGGTGGCTTTGGGGGTTGGGATGGAGGCAGAGG
AGGCCAAGGTGGTGGCAGAGGAGGCTGAGGCAGATTTGGTGGCAGAGGCCAGGGAGGCTTTGGAGGCTGAGGAGGCTTCT
GAGGTGGAAGAGGAGGAGACCACAAGCCACAAGGAAAGACGAAGTTTGAA

Alignment

ORF - retro_ogar_1417 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.24 %
• Parental protein coverage: 61.72 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAFDLFTKFGYVDFESAEDLEK-ALELTGLKVFGNEIKLEKPKGKDSKKDRDARTLLAKNLPYKVTQDEL
          V......KFGYVDF.S.EDLEK.AL.LTGLKVFGNEI.LEKPKGKDSKK.RD.RTLLA.NLP.KVTQDEL
Retrocopy VRIGMTRKFGYVDFDSVEDLEK<ALQLTGLKVFGNEIELEKPKGKDSKKERDTRTLLAQNLPSKVTQDEL

Parental  KEVFEDAMDIRIVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYTGEKGQNQDYRGGKNS
          KEVFE.AM.IRIVSK.GKS.GIA.IEFKTEADAEKTFEEKQGTEI...SISLYYTGEKGQ.QDY.GGKNS
Retrocopy KEVFEGAMEIRIVSKNGKSTGIANIEFKTEADAEKTFEEKQGTEIAW*SISLYYTGEKGQSQDYGGGKNS

Parental  TWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIE
          TWS.ESKTLVLS.LSYSATEETLQEVFEKA.FIK.P.NQ.GKSKGYAFIEFASFED.KEALNSCNKREIE
Retrocopy TWSYESKTLVLSKLSYSATEETLQEVFEKASFIKAPPNQMGKSKGYAFIEFASFEDTKEALNSCNKREIE

Parental  -GRAIRLELQAPRGSPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFN
          .GRAIRLEL.APRGSPNA.SQPSK.LFVKGLSEDTT.ETLKESFD.SV.A.IVTDRE.GSSKGF.F..FN
Retrocopy <GRAIRLELEAPRGSPNA*SQPSKALFVKGLSEDTTGETLKESFDSSVHAQIVTDREPGSSKGFEFLNFN

Parental  SEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGFGGRGGGRGGRGGGRGGRGGFGGRGRGGFGGRGGFR
          SEEDAKAAKEAME.GE.DGNKVTLDW.KPK.EGGFGG..GGRGG.GGGRGG.G.FGGRG.GGFGG.GGF.
Retrocopy SEEDAKAAKEAMENGETDGNKVTLDWVKPKDEGGFGGWDGGRGGQGGGRGG*GRFGGRGQGGFGG*GGF*

Parental  GGRGGGDHKPQGKKTKFE
          GGR.GGDHKPQG.KTKFE
Retrocopy GGR-GGDHKPQG-KTKFE

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_1417 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016174	1 retrocopy	retro_btau_1713,
Myotis lucifugus	ENSMLUG00000014547	1 retrocopy	retro_mluc_685,
Otolemur garnettii	ENSOGAG00000027852	1 retrocopy	retro_ogar_1417 ,
Tursiops truncatus	ENSTTRG00000009094	2 retrocopies	retro_ttru_1887, retro_ttru_51,