RetrogeneDB ID: retro_gmor_17

Retrocopy location

• Organism: Cod (Gadus morhua)
• Coordinates: GeneScaffold_3776:501613..502705(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGMOG00000020044
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: POU3F3 (1 of 2)
• Ensembl ID: ENSGMOG00000015654
• Aliases: None
• Description: POU class 3 homeobox 3 [Source:HGNC Symbol;Acc:9216]

Sequence

>retro_gmor_17
ATGGCCACAGCTGCCTCCAGCCCCTACACCCTGCTCAGTTCCAGCCCCATGATCCACCCCGACAGCCAGGCCATGCAGCC
GGCCAGTCCCTACAGGAGCCACCCCAAGCTCATGCAGAGCGACTACCTGCAGAGCGTCCAGAGCAACGGCCATTCCCTGG
GGCACCAGTGGGCGAGCAGCCTGTCGGAGGGCAGCCCCTGGTCGGCCTCCATGGAGCAACAGGACATCAAACCCGGCCGG
GAGGACCTTCAGCTCGGCATCATCCATCACCGCTCGCAGCACGTAGCGCACCACTCGCCCCATCACAACAACCATGCCAA
CCATCCGGGTGTCTGGGGCACTCAGGTGTCCCACAACTCCTCCATCAACAGTGGGCAGCAGCTCAACCTCTACTCCCAGA
CGGGCTTCACGGTCAACGGCATGCTGGAGCACGGCGGCCTCACACCTCCGTCTAATCAGCAGGGCCAGGGCATGCACCCC
GGCCTCAGGGACACGCTCAGCCCCGATCACAGCGACCTCGGCGGGCACCACTGCCACGACCACTCCGACGAAGAGACGCC
CACTTCGGACGAACTGGAGCACTTTGCCAAACAGTTCAAACAGCGGAGAATTAAGCTGGGCTTTACGCAGGCCGACGTGG
GTCTGGCACTGGGCACTCTGTACGGCAACGTTTTTTCCCAGACCACCATCTGCAGGTTCGAGGCTCTGCAGCTGAGCTTT
AAAAACATGTGCAAGTTAAAGCCGCTGCTGAACAAGTGGCTGGAGGAGGCGGACTCGTCGACGGGCAGCCCCAGCAGTAT
AGACAAGATAGCAGCTCAGGGCAGGAAGAGGAAGAAGAGGACGTCCATCGAAGTCAGCGTGAAGGGGGTTTTGGAGACGC
ACTTTCTGAAATGTCCCAAGCCCTCCGCGCAGGAGATTACCTCGCTCGCGGACTCGCTGCAGCTGGAGAAGGAGGTGGTG
CGCGTGTGGTTCTGCAACCGACGGCAGAAGGAGAAGCGCATGACGCCACCAGGAGAGCCTCCGATGCACGAGGGACCGTA
TTCTCACGGCGGCGGGAGCGCGGGAGACGCTTCGTCGTGCCATGATCTCTGA

Alignment

ORF - retro_gmor_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.5 %
• Parental protein coverage: 51.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VHAGLVRGDTPDLDHGGSNNSHEVHSDEDTPTSDDLEQFAKQFKQRRIKLGFTQADVGLALGTLYGNVFS
          .H.GL.....PD....G....H..HSDE.TPTSD.LE.FAKQFKQRRIKLGFTQADVGLALGTLYGNVFS
Retrocopy MHPGLRDTLSPDHSDLGGHHCHD-HSDEETPTSDELEHFAKQFKQRRIKLGFTQADVGLALGTLYGNVFS

Parental  QTTICRFEALQLSFKNMCKLKPLLNKWLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEVSVKGALESHFL
          QTTICRFEALQLSFKNMCKLKPLLNKWLEEADS.TGSP.SIDKIAAQGRKRKKRTSIEVSVKG.LE.HFL
Retrocopy QTTICRFEALQLSFKNMCKLKPLLNKWLEEADSSTGSPSSIDKIAAQGRKRKKRTSIEVSVKGVLETHFL

Parental  KCPKPSAQEITSLADNLQLEKEVVRVWFCNRRQKEKRMTPPGVPQTPEDVYSQVGNASAD
          KCPKPSAQEITSLAD.LQLEKEVVRVWFCNRRQKEKRMTPPG.P...E..YS..G....D
Retrocopy KCPKPSAQEITSLADSLQLEKEVVRVWFCNRRQKEKRMTPPGEPPMHEGPYSHGGGSAGD

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_17 retrocopy.

TSS

Gadus morhua was not studied using FANTOM5 data.

Lab

retro_gmor_17 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	ENSGMOG00000015654	1 retrocopy	retro_gmor_17 ,