RetrogeneDB ID: retro_gmor_19

Retrocopy location

• Organism: Cod (Gadus morhua)
• Coordinates: GeneScaffold_2432:1771..2394(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSGMOG00000009026
• Aliases: None
• Description: None

Sequence

>retro_gmor_19
AGGAACGGGGCCCTTTCTCCATCTTTACAAGTGTGTCTAGCACTCAGATACTTTGCCACCGGTTCATTTCAAAGTCTTGT
GGGGGACTCAATACAGGTACACAAGTCCACTGTTTGTAGGACAGTCCGCTCTGTGGCACTGTCATTATGCAGACGCATTA
ACACCTTCGTCGGTTTCTCATCCCAACCTGACCAACAAATCATCGCACGTCAGAAGTTTTTTAACATCGCTGGATTCCCT
GACGTGCTGGGCTGTGTGGATGGGACTCACATCAGGATCAAAACCCCCACGGAGCATGAAAATGTATTCGTCAACAGAAA
AGGCTATCACTCGATCAATGCCCAGATAGTGTGTGACGCTGACCTCAAAATAACAAACTGCGTGATCAAGTGGCCTGGGT
CTAAACACGACAGTTATATTCTAAGGCAATCCAGGCTTTGGGGGAATTCGAGGCAGGCACTTATCCAGGGAGACTCCTGG
GGGACTCGGGCTATCCTCTCAGGCCGTGGCTGATGACTCCATACCTCAACCCAGCCAATTACCACGAAGAGCGCTACAAC
TCAGCGCACATAAAAACCAGGAATGCGGTGGAGAGGTGTATTGGAGTTCTTAAAAAGCGCTGG

Alignment

ORF - retro_gmor_19 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.24 %
• Parental protein coverage: 97.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RGHALSSIQIICVALRFFANGSFLYNVGDAEHISKATVCRSVRNVTLALKRFLYTFVMFPSHRPIRTI-K
          R..ALS.....C.ALR.FA.GSF...VGD.....K.TVCR.VR.V.L.L.R...TFV.F.S......I..
Retrocopy RNGALSPSLQVCLALRYFATGSFQSLVGDSIQVHKSTVCRTVRSVALSLCRRINTFVGFSSQPDQQIIAR

Parental  EEFYRIADFPGVIGCIDGTHIPIKAPSVHEGDYVNRKSFHSINVQVVCDARNIITQVEAKWPGSVHDARI
          ..F..IA.FP.V.GC.DGTHI.IK.P..HE...VNRK..HSIN.Q.VCDA...IT....KWPGS.HD..I
Retrocopy QKFFNIAGFPDVLGCVDGTHIRIKTPTEHENVFVNRKGYHSINAQIVCDADLKITNCVIKWPGSKHDSYI

Parental  FRESNL-STRFAIGEFDGHVLGDRGYPCQPCLLTPYADPVPGPQQRYNLAHMRTRARVENTFGILKARF
          .R.S.L....F..G...G..LGD.GYP..P.L.TPY..P......RYN.AH..TR..VE...G.LK.R.
Retrocopy LRQSRL<LGEFEAGTYPGRLLGDSGYPLRPWLMTPYLNPANYHEERYNSAHIKTRNAVERCIGVLKKRW

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_19 retrocopy.

TSS

Gadus morhua was not studied using FANTOM5 data.

Lab

retro_gmor_19 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000017629	1 retrocopy	retro_gacu_21,
Gadus morhua	ENSGMOG00000009026	1 retrocopy	retro_gmor_19 ,
Gadus morhua	ENSGMOG00000012106	1 retrocopy	retro_gmor_30,
Gadus morhua	ENSGMOG00000012261	1 retrocopy	retro_gmor_35,