RetrogeneDB ID: retro_gmor_7

Retrocopy location

• Organism: Cod (Gadus morhua)
• Coordinates: GeneScaffold_4578:172916..173972(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGMOG00000020380
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RHO (2 of 2)
• Ensembl ID: ENSGMOG00000013755
• Aliases: None
• Description: rhodopsin [Source:HGNC Symbol;Acc:10012]

Sequence

>retro_gmor_7
ATGAACGGCACAGAGGGACCTGCCTTCTATGTGCCCTGGGACAACAGCACTGGCATCGTGCGGAGCCCCTATGAGTACCC
CCAGTACTACCTGGTCTCAACGGCGGCCTACTCCGCCCTGGCCGCCTACATGTTCCTACTCATCCTGCTCGGCTTCCCCA
TCAACTTCCTCACCCTCTACGTCACCCTGGAACACAAGAAGCTGCGGACGCCCCTGAACTACATCCTGCTGAACATGGCC
GTGGCCAACCTGTTCATGGTTTTCGGCGGCTTCACCACCACCATGTACACCTCCATGCACGGCTACTTCGTCTTAGGGCG
CACCGGCTGCAACATCGAAGGATACTTTGCCACCCTGGGCGGTGAGATCGGGCTGTGGTCGCTGGTGGTGTTGGCCATCG
AGCGCTGGGTCGTCGTCTGCAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCACGCCGTCATGGGCGTGGCCTTCACC
TGGGTCATGGCCAACGCTTGCGCTTTCCCCCCCCTGGTGGGCTGGTCTCGTTACATCCCCGAGGGAATGCAGTGCTCATG
CGGAGTCGACTACTACACTCGCGCCGAGGGCTACAACAACGAGTCTTTCGTCATCTATATGTTCACATGCCACTTCCTGA
CCCCCATGTTCGTGATCTTCTTCTGCTACGGACGGCTGCTCTGCGCAGTGAAGGAGGCTGCCGCCGCCCAGCAGGAGTCC
GAGACCACCCAGAGAGCGGAGAGGGAGGTGAGCCGCATGGTGGTCATCATGGTGTTGGGCTTCCTGATCTGCTGGGTTCC
CTACGCCAGCGTGGCCTGGTACATCTTCTGCAACCAGGGCAGCATCTTCGGTCCCATCTTCATGACCCTGCCGGCTTTCT
TTGCCAAGTCCTCGTCCATCTACAACCCCCTGATCTACATCTGCATGAACAAGCAGTTCCGTCACTGCATGATCACCACC
CTGTGCTGCGGCAAGAACCCCTTCGAGGAGGAGGAAGGATCCAGCGCCAAGACCGAGGCCTCCTCCGTCTCCACCAGCTC
CGTGTCCCCCGCGTAA

Alignment

ORF - retro_gmor_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNGTEGPNFYVPMSNKTGVVRSPFEHPQYYLAEPWKYSLVAAYMLFLIATAFPVNFLTLYVTVKNKKLRT
          MNGTEGP.FYVP..N.TG.VRSP.E.PQYYL.....YS..AAYM..LI...FP.NFLTLYVT...KKLRT
Retrocopy MNGTEGPAFYVPWDNSTGIVRSPYEYPQYYLVSTAAYSALAAYMFLLILLGFPINFLTLYVTLEHKKLRT

Parental  PLNYILLNLAVADLFMVVGGFTVTLYTALHGYFVLGVGGCNIEGFFATLGGEIALWSLVVLAVERYVVVC
          PLNYILLN.AVA.LFMV.GGFT.T.YT..HGYFVLG..GCNIEG.FATLGGEI.LWSLVVLA.ER.VVVC
Retrocopy PLNYILLNMAVANLFMVFGGFTTTMYTSMHGYFVLGRTGCNIEGYFATLGGEIGLWSLVVLAIERWVVVC

Parental  KPMSNFRFEEKHAVAGLAFTWVMALTCAGPPLFGWSRYIPEGMQCSCGIDYYTPKPEINNTSFVIYMFLL
          KPMSNFRF.E.HAV.G.AFTWVMA..CA.PPL.GWSRYIPEGMQCSCG.DYYT.....NN.SFVIYMF..
Retrocopy KPMSNFRFGENHAVMGVAFTWVMANACAFPPLVGWSRYIPEGMQCSCGVDYYTRAEGYNNESFVIYMFTC

Parental  HFLIPLFVIFFCYGRLLCTIRAAAALQQESESTQRAEKEVTRMVIVMVISFLVCWVPYATVAWYIFINQG
          HFL.P.FVIFFCYGRLLC....AAA.QQESE.TQRAE.EV.RMV..MV..FL.CWVPYA.VAWYIF.NQG
Retrocopy HFLTPMFVIFFCYGRLLCAVKEAAAAQQESETTQRAEREVSRMVVIMVLGFLICWVPYASVAWYIFCNQG

Parental  AEFGPVFMTAPAFFAKSAALYNPVIYILCVSQFRNCMLTTVCCGRNPFREEDTGLSSKTQSSTISTSQVA
          ..FGP.FMT.PAFFAKS...YNP.IYI....QFR.CM.TT.CCG.NPF.EE..G.S.KT..S..STS.V.
Retrocopy SIFGPIFMTLPAFFAKSSSIYNPLIYICMNKQFRHCMITTLCCGKNPFEEEE-GSSAKTEASSVSTSSVS

Parental  PA
          PA
Retrocopy PA

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_7 retrocopy.

TSS

Gadus morhua was not studied using FANTOM5 data.

Lab

retro_gmor_7 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gadus morhua	ENSGMOG00000013755	1 retrocopy	retro_gmor_7 ,
Oreochromis niloticus	ENSONIG00000017219	1 retrocopy	retro_onil_16,
Oryzias latipes	ENSORLG00000010979	1 retrocopy	retro_olat_6,
Tetraodon nigroviridis	ENSTNIG00000017925	1 retrocopy	retro_tnig_20,
Takifugu rubripes	ENSTRUG00000010617	1 retrocopy	retro_trub_18,
Xiphophorus maculatus	ENSXMAG00000017297	1 retrocopy	retro_xmac_11,