RetrogeneDB ID: retro_gmor_1

Retrocopy location

• Organism: Cod (Gadus morhua)
• Coordinates: GeneScaffold_4354:9876..10863(-)
• Located in intron of: ENSGMOG00000000005

Retrocopy information

• Ensembl ID: ENSGMOG00000019748
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KCNJ10
• Ensembl ID: ENSGMOG00000012121
• Aliases: None
• Description: potassium inwardly-rectifying channel, subfamily J, member 10 [Source:HGNC Symbol;Acc:6256]

Sequence

>retro_gmor_1
CAGCGGCGCATCGTTTCCAAGGACGGCCACAACAACGTGAGGATCGACAACGTGGAAGGCATGGTCAAGCTGTACCTGCA
CGACATCTGGACTACCGTGGTGGACATGAAGTGGCGCTACAAACTCACTCTGTTCGCCTCCACCTTCGTCATGACCTGGT
TCTTTTTCGGGGTTATCTTCTACTTCATCAGCATGGGAAACGGGGACTTTGAGGCGGTGCTGCCGTCCAACCACACGCCC
TGCGTGGAGAACGCCAAGACGCTGACCGGCGCCTTCCTCTTCTCCCTGGAGTCGCAGACCACCATCGGCTATGGCTTCCG
CTACATTAACGAGGAATGCCCTCTGGCCATCTTCACCCTGGTGGCTCAGCTGGTGATCACCGGACTGGCAGAGATCTTCG
TCACCGGGGCTTTCCTGGCCAAGCTGGCTCGGCCCAAGAAGCGCGCCGAGACCATCAAGTTCAGCCGCTCGGCGGTGGTG
TGCCGGCGGGAGGGGAAGCTGTGCATCATGGTGCGCGTGGCCAACATGAGGAAGAGCTTGCTAGTCCAGTGCCAGCTCAC
GGGCAAGCTCCTCCACCCAAAGGTGACGCAGGAGGGCGAGAAGACACTGGTGCACCAGAGCAGCGTCAACTTCTACATGG
ACTCCAGCGGCGAGTGCCCCTTCCTCATCCTGCCCCTGACCTTCTACCACGTGCTGGACGAGAGCAGCCCCCTTGTGGGC
CTGACGGCCGACAACCTGCACACCCGAGACTTTGAGCTGCTGGTGACCCTGAACGCCACCATGGAGTCAACGGCTGCCAC
CTGCCAGAGCCGCACGTCCTACGTGCCCCAGGAGATCCTGTGGGGCTACGAGTTCAAGCCGGTGCTCTTCAGCAACAACA
ACAGCCGCTATGTGGCCGACTTCAGCTTCTTTGATAAAGTGCAGGCGAGCGCTGATTCCATGTTTCTTAGCAACAACACA
GAGAAGCTCAAGCTGGAGGAAGAATAT

Alignment

ORF - retro_gmor_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.83 %
• Parental protein coverage: 56.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRRVLSKDGRSNVLIEHVSGRSALYLRDLWTTFLDMQWRYKLFLFSATFAGTWFLFGLLWYLVALVHGDL
          .RR..SKDG..NV.I..V.G...LYL.D.WTT..DM.WRYKL.LF..TF..TWF.FG...Y......GD.
Retrocopy QRRIVSKDGHNNVRIDNVEGMVKLYLHDIWTTVVDMKWRYKLTLFASTFVMTWFFFGVIFYFISMGNGDF

Parental  LEFDPLPSNHTPCVMEMRTLTGAFLFSLESQTTIGYGFRCITEECPHAIILLIVQLVITMVMEIFITGTF
          .....LPSNHTPCV....TLTGAFLFSLESQTTIGYGFR.I.EECP.AI..L..QLVIT...EIF.TG.F
Retrocopy EAV--LPSNHTPCVENAKTLTGAFLFSLESQTTIGYGFRYINEECPLAIFTLVAQLVITGLAEIFVTGAF

Parental  LAKVARPKKRGETVKFSQYALVSNYQGRPCLMIRVANMRKSLLLGCQVTGKLLQTSLTKEGETVRLDQQN
          LAK.ARPKKR.ET.KFS..A.V....G..C.M.RVANMRKSLL..CQ.TGKLL....T.EGE.....Q..
Retrocopy LAKLARPKKRAETIKFSRSAVVCRREGKLCIMVRVANMRKSLLVQCQLTGKLLHPKVTQEGEKTLVHQSS

Parental  VPFQVDTSSDSPFLIIPLTFYHVIDHTSPL
          V.F..D.S...PFLI.PLTFYHV.D..SPL
Retrocopy VNFYMDSSGECPFLILPLTFYHVLDESSPL

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_1 retrocopy.

TSS

Gadus morhua was not studied using FANTOM5 data.

Lab

retro_gmor_1 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gadus morhua	ENSGMOG00000009508	1 retrocopy	retro_gmor_6,
Gadus morhua	ENSGMOG00000012121	1 retrocopy	retro_gmor_1 ,
Tetraodon nigroviridis	ENSTNIG00000006226	1 retrocopy	retro_tnig_21,