RetrogeneDB ID: retro_gmor_20

Retrocopy location

• Organism: Cod (Gadus morhua)
• Coordinates: GeneScaffold_3222:273246..274278(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGMOG00000016770
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: sfpq (2 of 2)
• Ensembl ID: ENSGMOG00000011950
• Aliases: None
• Description: splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated) [Source:ZFIN;Acc:ZDB-GENE-040426-2452]

Sequence

>retro_gmor_20
CCAGAGCCGAACGAGGCCCTGACCCTGGATCTGCAAAACTTCCGAAAACCCGGAGAAAAGGCCTACACCCAACGTAGCAG
GCTGTTCGTGGGGAACCTCCCGACGGGAGTGTCCGAGCCAGAGGTGGAGAAGCTGTTCTCCAAGTACGGCAAGCCCTCCG
AGATCTTCATCAACAAAGACCGGGGCTTCGGGTTCATCCGGCTTGAGTCGCGGATCATCGCCGAGATCGCCCGAGCCGAG
CTCGACGATACCCCGTTCAGAGGCAGGCAGATCCGGGTTCGCTTCGCGACCCACGGCGCCGCGTTGACCGTGAAGAATCT
GCCCGATTTCGTGTCAAACGAGCTGCTGGAGGAGGCCTTCGCCGTGTTCGGCCAGATCGAGAGAGCCATAGTGATCGTGG
ATGACAGGGGACGGCCCACGGGGAAAGGCATCGTGGAGTACACCTCCAAGCCAGCCGCCAGGAAGGCGTTGGATAAGTGC
GGCGAGGGTGCATTCCTGCTGACCGCCTTCCCCAGACCCGTGACGGTGGAGCCCATGGATCAGTTCGACGACGACGAGGG
CTTGTCAGAGAAGCTGGTGAACAAGAACCAGCAGTACCACAAAGAGCGAGAGCAGCCGCCGCGGTTCGCCCAGCCAGGGA
CCTTCGAGTACGAGTACGCCATGCGCTGGAAGGCCCTGATGGAGATGGAGAAGCAGCAGTACGACATGGTGGACCGTAAC
ATCAAGGAGGCCCACGAGAAGCTGGAGCAGGAGATGGAGGCTGCCCGACACGAGCACCAGGTGATCCTCATGAGGCAGGA
CCTGCTCCGCCGCCAGGAGGAGCTCAGGAGGATGGAGGAACTCCACAGTCAGGAGATGCAGAAGCGAAAGCAGGCCGAGA
TCCGACAGGAGGAGGACAGGCGTCGGCGAGAGGAGGAGGTGAGGATGCGCGGGGAGGAGATGATGAAGAGGCAGCAGGAG
GGATTCAGGGGGAACTTCCCTGAAGGCAGGGAGCAAGAGATGAGGATGCATATGGCTGGCGGCCACGGGATG

Alignment

ORF - retro_gmor_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.05 %
• Parental protein coverage: 61.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKPNQELKATLSLLLKPGEKTYTQRCRLFIGNLPNDISDEEFKKLFAKYGEPSEVFINKNKGFGFIRLES
          P.PN..L...L....KPGEK.YTQR.RLF.GNLP...S..E..KLF.KYG.PSE.FINK..GFGFIRLES
Retrocopy PEPNEALTLDLQNFRKPGEKAYTQRSRLFVGNLPTGVSEPEVEKLFSKYGKPSEIFINKDRGFGFIRLES

Parental  RALAEIAKAELDDTPMKGRPLRVRFATHSAALSIKNLSPFVSNELLEEAFSQFGMVERAVVIVDDRGRSS
          R..AEIA.AELDDTP..GR..RVRFATH.AAL..KNL..FVSNELLEEAF..FG..ERA.VIVDDRGR..
Retrocopy RIIAEIARAELDDTPFRGRQIRVRFATHGAALTVKNLPDFVSNELLEEAFAVFGQIERAIVIVDDRGRPT

Parental  GKGLVEFASKPAARKALDRCNEGVFLLTTSPRPVVVEPLEQYDDEDGLPEKLAQKNPRYQKEREEPPRFA
          GKG.VE..SKPAARKALD.C.EG.FLLT..PRPV.VEP..Q.DD..GL.EKL..KN..Y.KERE.PPRFA
Retrocopy GKGIVEYTSKPAARKALDKCGEGAFLLTAFPRPVTVEPMDQFDDDEGLSEKLVNKNQQYHKEREQPPRFA

Parental  RPGTFEFEYSKRWKSLDEMEKQQRQQVDKNMREAREKLESEMEDAFHEHQANLLRQDLLRRQEELRRMEE
          .PGTFE.EY..RWK.L.EMEKQQ...VD.N..EA.EKLE.EME.A.HEHQ..L.RQDLLRRQEELRRMEE
Retrocopy QPGTFEYEYAMRWKALMEMEKQQYDMVDRNIKEAHEKLEQEMEAARHEHQVILMRQDLLRRQEELRRMEE

Parental  MHSQEMLKRKEMQIRQEEERRRREEEMIHKREVEEQMRRQREEKYRGMGNFMESRERDMRMNQGGAMGL
          .HSQEM.KRK...IRQEE.RRRREEE.......EE.M.RQ..E..RG..NF.E.RE..MRM...G..G.
Retrocopy LHSQEMQKRKQAEIRQEEDRRRREEEV--RMRGEEMMKRQ-QEGFRG--NFPEGREQEMRMHMAGGHGM

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_20 retrocopy.

TSS

Gadus morhua was not studied using FANTOM5 data.

Lab

retro_gmor_20 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003595	1 retrocopy	retro_cfam_198,
Callithrix jacchus	ENSCJAG00000001431	4 retrocopies	retro_cjac_1073, retro_cjac_2542, retro_cjac_2697, retro_cjac_486,
Felis catus	ENSFCAG00000031287	1 retrocopy	retro_fcat_1989,
Gasterosteus aculeatus	ENSGACG00000002034	1 retrocopy	retro_gacu_13,
Gadus morhua	ENSGMOG00000011950	1 retrocopy	retro_gmor_20 ,
Macropus eugenii	ENSMEUG00000014082	1 retrocopy	retro_meug_164,
Oryctolagus cuniculus	ENSOCUG00000001877	1 retrocopy	retro_ocun_1834,
Oreochromis niloticus	ENSONIG00000017737	1 retrocopy	retro_onil_21,
Sarcophilus harrisii	ENSSHAG00000016107	1 retrocopy	retro_shar_36,
Tetraodon nigroviridis	ENSTNIG00000011331	1 retrocopy	retro_tnig_32,
Takifugu rubripes	ENSTRUG00000003783	1 retrocopy	retro_trub_8,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,