RetrogeneDB ID: retro_gmor_36

Retrocopy location

• Organism: Cod (Gadus morhua)
• Coordinates: scaffold11281:234..1044(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THAP9 (1 of 3)
• Ensembl ID: ENSGMOG00000017324
• Aliases: None
• Description: THAP domain containing 9 [Source:HGNC Symbol;Acc:23192]

Sequence

>retro_gmor_36
AGGTGGATGATCTCTGTGGATTCCAAGCCTGGACTCAACACCATGATGCTGGACATGTTGAGAAGAAAAAGAGAGGAAGA
TCCAGTGAAGTATGGACGTGTGGCGCTCATGCTGGATGGCATGGCCATCAGGAAACATGTCCAGTACAGTCCACATTCCC
AGAAAATGACCGGATTTGTGGACATGGGGGATGGCCTAAACGAGACAGATATTGCCACTGAGGCTCTGGTTTTTATGGTG
GTTGGCCTACAAGGCCATTGGAAGGCTCCAATTGCCTACTACCTGACCAAGTCTCTGACGCCCGACACACAGAAGGTCCT
GCTGGTACATGCGCTGGAGGCCCTGCATGAGCGTGGCATCCGGGTCATGTCCCTCACAATGGATGGGCATGCATCAAACG
TAAGCATGTGCAACCAGCTGGGGTGCCAGCTAAAGGCCAACCCTTGTGAGCCTTTGAAAACATTTTTCCCCCATCCTGCG
ACTGGCGAGAGGGTGTTTGTCATGATGGACGCTTGCCACATGTTGAAGCTGGCAAGAAACATGCTGCAAGCGTACAGCCC
AATCTGTAGCAGAACTGGCCTCATCAACTGGGACTACGTTGTTTGTTTGAACGATATTCAAACAAAGAATGGACTGCATG
CTGCCAACAGGGTCACTGAAAAGCACATTCAGTTTGACTCACAGAAGATGAAGGTGTCCCTGGCTGCACAGACGCTGAGT
CGCTCTGTGGCAGTAGCGCTCCGAACGCTGAGGGACCTGGGGTATCCACGCTTCACCCTCTCTCTAGCGACAGCCGAATT
CATTGAGGTA

Alignment

ORF - retro_gmor_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.56 %
• Parental protein coverage: 79.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RWLSSLDERPGLNTMMLNMLGRKFEEDPDKHGHVTLMLDAMSIKKLLQYNPRTNRMSGYVDLGNGCNETD
          RW..S.D..PGLNTMML.ML.RK.EEDP.K.G.V.LMLD.M.I.K..QY.P....M.G.VD.G.G.NETD
Retrocopy RWMISVDSKPGLNTMMLDMLRRKREEDPVKYGRVALMLDGMAIRKHVQYSPHSQKMTGFVDMGDGLNETD

Parental  PATEALVLMVVGLKGHWNAPIGYFFTSTLTADTQKELVVQALEALHDRSIKVVNITMDGHATSLGICNLL
          .ATEALV.MVVGL.GHW.API.Y..T..LT.DTQK.L.V.ALEALH.R.I.V...TMDGHA.....CN.L
Retrocopy IATEALVFMVVGLQGHWKAPIAYYLTKSLTPDTQKVLLVHALEALHERGIRVMSLTMDGHASNVSMCNQL

Parental  RTNLKGNPKDPLKTSFTHPSSGDEVFVIMDECHMLKLARNMLESYRTINSGSGRIEWKHIVELNNVQKKE
          ...LK.NP..PLKT.F.HP..G..VFV.MD.CHMLKLARNML..Y..I.S..G.I.W...V.LN..Q.K.
Retrocopy GCQLKANPCEPLKTFFPHPATGERVFVMMDACHMLKLARNMLQAYSPICSRTGLINWDYVVCLNDIQTKN

Parental  GLDADSQRTDRYSCQFQQPKNEGLFVFVFVNSVAVALRTLKDLGYEQLNDCEATVEFLQM
          GL.A....T........Q.....L.......SVAVALRTL.DLGY.......AT.EF...
Retrocopy GLHAANRVTEKHIQFDSQKMKVSLAAQTLSRSVAVALRTLRDLGYPRFTLSLATAEFIEV

Legend:

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

Expression

RNA-Seq

Gadus morhua was not studied using RNA-Seq expression data.

ChIP-Seq

Gadus morhua was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_gmor_36 retrocopy.

TSS

Gadus morhua was not studied using FANTOM5 data.

Lab

retro_gmor_36 was not experimentally validated.

Homology

Retrocopy orthology:

Gadus morhua 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Gadus morhua	ENSGMOG00000017324	1 retrocopy	retro_gmor_36 ,