RetrogeneDB ID: retro_ogar_2862

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873672.1:4604046..4605333(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX1
• Ensembl ID: ENSOGAG00000008730
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 1 [Source:HGNC Symbol;Acc:2734]

Sequence

>retro_ogar_2862
CTGAATAACATCAAGCAGTTTAAGAAATATATTGATAGTCCTAAATTAAGGGAGCTTCTGATAATTGGAGGTGTTGCAGC
ACAGGACCAGCTCTCGGTTTTGGAAAATGGGGTAGATATAGTTGTAGGCACTCCAGGAAGAATGGATGACTTGATGTCAA
CTGGAAAACTGAACTTATCTCAAGTTAGATTTCTGGTCCTCCAAGAAGCTGATGGGCTGCTTTCTCAAGGTTAATCTGAC
TTTATAAATAGGATGCACAATCAGATTCCTCAGATTACCTCTGATGGAAAAAGACTTCAGGTGATTGTTTGCTCTGTCAC
TTTGCATTCTTTTAATGTAAAGAAATTATCTGAAAAGATAATGCATTTTCCTATGTGAGTTGATTTAAAAGAAGATTCTG
TTCCAGATACTGTACACCAAGTTGTTGTTCCAGTGAATCCCAAAACTGACAGACTCTGGGAAAGGCTTGGAATGAACCAC
ATTAGAACTGGTGATGTACATGCAAAGATAACACAAGACCTGATGCTAATAGTCTGGAAATGTAGTATGAAGCTGTTAAA
ATTCTGAAGGGGGGAGTATACTGTCTGGCAATCAAGGAACACAAAAAGGATCAAACAATTATCTTCTATAGAACCAAGAT
TGACTGTGATAACTTGGAGCAATATTTTGTGCAACAAGGAGGAGGACCTGATAAAAAGGGGCACCAGTTCTTATGTGTTT
ATCTTCATGGTGACAGAAAGTGTCATGAGAGAAAGAAAAACTTGGAAAGATTTAAGAAAGGAGATGTAAGATTCTGCACA
GATGTAGCTGCTAGCGGAATTGATATTCATGGTGTTCCTTATGTTACAAATGTCACTCTACCTGATGAAAAGCAAAACTA
CGTACATTGAATTGGCAGAGTAGGAAGAGCGGAAAGAATGGGTCTGGCCATTTCCCTGGTGGCATCAGAGAAAGAAAAGG
TTTGGTACCCTGTATGTAGCAGCCGTGGAAAGGAGTATTACAACACAAGACTCAAGGAAGACGGAGGCTGTACCATATGG
TACAATGAGATGCAGTTTACTATCTGAGAAAGAACACCTGAACTATACCATTTCTCAAGTTGAGCCAGATATAAAGGTAC
CAGTGGATGAATTTGATGGAAAAGTTACCTATGGTCAAAAAAGGGCTGCTGGTGGTGGAATTTATAAATGCCATGTGGAT
ATTTTGACACCTACCATTCAAGAGTTGGTTTCCCTTGAAAAAGAAGCACAGACTCGGCGCCTATAGCTCAACCGGCTAAG
ACGCCAG

Alignment

ORF - retro_ogar_2862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.9 %
• Parental protein coverage: 58.83 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LNNIKQFKKYIDNPKLRELLIIGGVAARDQLSVLENGVDIVVGTPGRLDDLVSTGKLNLSQVRFLVLDEA
          LNNIKQFKKYID.PKLRELLIIGGVAA.DQLSVLENGVDIVVGTPGR.DDL.STGKLNLSQVRFLVL.EA
Retrocopy LNNIKQFKKYIDSPKLRELLIIGGVAAQDQLSVLENGVDIVVGTPGRMDDLMSTGKLNLSQVRFLVLQEA

Parental  DGLLSQGYSDFINRMHNQIPQITSDGKRLQVIVCSATLHSFDVKKLSEKIMHFPTWVDLKGEDSVPDTVH
          DGLLSQG.SDFINRMHNQIPQITSDGKRLQVIVCS.TLHSF.VKKLSEKIMHFP..VDLK.EDSVPDTVH
Retrocopy DGLLSQG*SDFINRMHNQIPQITSDGKRLQVIVCSVTLHSFNVKKLSEKIMHFPM*VDLK-EDSVPDTVH

Parental  HVVVPVNPKTDRLWERLGKNHIRTDDVHA-KDNTRPGANSPEMWSEAVKILKGEYTVRAIKEHKMDQAII
          .VVVPVNPKTDRLWERLG.NHIRT.DVHA.KDNTRP.ANS.EM..EAVKILKG.....AIKEHK.DQ.II
Retrocopy QVVVPVNPKTDRLWERLGMNHIRTGDVHA<KDNTRPDANSLEM*YEAVKILKGGVYCLAIKEHKKDQTII

Parental  FCRTKIDCDNLEQYFMQQGGGPDKKGHQFSCVCLHGDRKPHERKQNLERFKKGDVRFLICTDVAARGIDI
          F.RTKIDCDNLEQYF.QQGGGPDKKGHQF.CV.LHGDRK.HERK.NLERFKKGDVRF..CTDVAA.GIDI
Retrocopy FYRTKIDCDNLEQYFVQQGGGPDKKGHQFLCVYLHGDRKCHERKKNLERFKKGDVRF--CTDVAASGIDI

Parental  HGVPYVINVTLPDEKQNYVHRIGRVGRAERMGLAISLVASEKEKVWYHVCSSRGKGCYNTRLKEDGGCTI
          HGVPYV.NVTLPDEKQNYVH.IGRVGRAERMGLAISLVASEKEKVWY.VCSSRGK..YNTRLKEDGGCTI
Retrocopy HGVPYVTNVTLPDEKQNYVH*IGRVGRAERMGLAISLVASEKEKVWYPVCSSRGKEYYNTRLKEDGGCTI

Parental  WYNEMQ-LLSEIEEHLNCTISQVEPDIKVPVDEFDGKVTYGQKRAAGGGNYKGHVDILAPTVQELAALEK
          WYNEMQ.LLSE..EHLN.TISQVEPDIKVPVDEFDGKVTYGQKRAAGGG.YK.HVDIL.PT.QEL..LEK
Retrocopy WYNEMQ>LLSE-KEHLNYTISQVEPDIKVPVDEFDGKVTYGQKRAAGGGIYKCHVDILTPTIQELVSLEK

Parental  EAQTSFLHLGYLPNQ
          EAQT..L.L..L..Q
Retrocopy EAQTRRL*LNRLRRQ

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_2862 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000008254	1 retrocopy	retro_meug_555,
Myotis lucifugus	ENSMLUG00000003027	1 retrocopy	retro_mluc_1223,
Otolemur garnettii	ENSOGAG00000007978	1 retrocopy	retro_ogar_2861,
Otolemur garnettii	ENSOGAG00000008730	1 retrocopy	retro_ogar_2862 ,