RetrogeneDB ID: retro_trub_8

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_264:187282..188614(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000005554
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SFPQ
• Ensembl ID: ENSTRUG00000003783
• Aliases: None
• Description: None

Sequence

>retro_trub_8
ATGCAAGGAAACCGAGGCCCCCAGCAGAACCATGGCCCCAACCGTTCAGCGGAGCAGAAGAAGCCCGGGGGGACAAACAC
GAACGGGCAGCAGCCCGACTCCAGCGAGCAGAACAACTCCAATGAGGCCTTAACCCTGGACCTGCAAAGCTTCAGGAAGC
CCGGGGAGAAGACGTTTACGCAGCGGAGCCGGCTGTTCGTTGGGAACCTGCCCACCGGAGTGGCCGAGGAGGATCTGGAG
AGGCTGTTCGCCAAATACGGGAAGGCCAGTGAGATTTTCATCAACAAGGACCGGGGCTTCGGCTTCATTCGCCTGGAGAC
TCGGATCATCGCAGAGATCGCCAGAGCAGAGCTGGATGACACCCCGTTCCGTGGCAGGCCCATCCGAGTCCGGTTCGCCA
CGCACGGCGCTGCATTGACTGTGAAAAACCTGCCAGAGTTTGTGTCCAACGAGTTGCTGGAGGAGGCCTTCGCTGTCTTT
GGCCAGATCGAAAGAGCTGTGGTGGTGGTGGACGACCGAGGGCGGCCCACGGGGAAGGGCATCGTGGAGTACACCTCCAA
ACCCGCCGCCAGGAAGGCTCTGGACAAGTGCAACGATGGGTCCTACCTGCTCACAGCCTTCCCTCGGCCCGTTACCGTGG
AGCCCATGGATCAACTCGACGACGATGAAGGACTACCAGAGAAGCTGGTTAACAAAAACCAACAGTACCACAAAGAACGC
GAACAGCCGCCCCGGTTTGCGCAGCCCGGCACCTTCGAGTACGAGTACGCGATGCGCTGGAAGGCTCTGATGGAGATGGA
GAAGCAGCAGTACGAGATGGTGGATCGCAACATGAAGGAGGCTCAGGAGAAGCTGGAGGCGGAGATGGAGGCGGCCCGGC
ACGAGCATCAAGTGATGCTGATGAGGCAGGACCTGTTGAGGAGGCAGGAGGAGCTGCGCAGGATGGAGGAGCTCCACAAC
CAGGAGGTGCAGAAGAGGAAGCAGGCCGAGCTTCGGCAGGAAGAGGAGCGCCGCCGGAGGGAGGAGGAGATGAGGCTGCG
CAACGAAGAGATGATGAAGAGGCAGCAAGAGGGCTTCAGGGCGAACTTCTCTGAGAACAGAGAGCAGGATCTGCGGATGC
ACATGGGCAGTCACGGGATGCCCATGAACAGGAACAATCTGGCCGCCGCCGCCGGTGCCGCCGCCGCCCCAGGCATGGCT
TCGGAGAACGCTGCCATCATGTCGGGGCCCGGAAACAACAGTATTCCCGGTGGAGGCCAGGGGGTCTTCCCCAGAGGGGT
CCCCGGGCCTGGAGACTACGGGTCTGGGCCCAACAAGCAGCGCAGATTTTGA

Alignment

ORF - retro_trub_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.04 %
• Parental protein coverage: 67.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QGQRSGQQQGQKTAPMAMKRADGQETMDNPAAQAEGSQAKE-FKATLSMLLKPGEKRYTQRCRLFIGNLP
          QG.R..QQ..........K...G..T........E.....E.....L....KPGEK..TQR.RLF.GNLP
Retrocopy QGNRGPQQNHGPNRSAEQKKPGGTNTNGQQPDSSEQNNSNEALTLDLQSFRKPGEKTFTQRSRLFVGNLP

Parental  NDITEEAFKKLFAKYGEPSEVFINKGKGFGFIRLESRALAEIAKAELDDTPMKGRPLRVRFATHSAALSV
          ....EE....LFAKYG..SE.FINK..GFGFIRLE.R..AEIA.AELDDTP..GRP.RVRFATH.AAL.V
Retrocopy TGVAEEDLERLFAKYGKASEIFINKDRGFGFIRLETRIIAEIARAELDDTPFRGRPIRVRFATHGAALTV

Parental  KNLSPFVSNELLEEAFSQFGMVERAVVIVDDRGRSTGKGIVEFASKPAARKALDRCSEGVFLLTCSPRPV
          KNL..FVSNELLEEAF..FG..ERAVV.VDDRGR.TGKGIVE..SKPAARKALD.C..G..LLT..PRPV
Retrocopy KNLPEFVSNELLEEAFAVFGQIERAVVVVDDRGRPTGKGIVEYTSKPAARKALDKCNDGSYLLTAFPRPV

Parental  VVEPLEQFDDEDGLPEKLAQKNPRYQAEREEPPRFARPGTFEFEYAKRWKSLDEMEKQQRQQVEKNMQEA
          .VEP..Q.DD..GLPEKL..KN..Y..ERE.PPRFA.PGTFE.EYA.RWK.L.EMEKQQ...V..NM.EA
Retrocopy TVEPMDQLDDDEGLPEKLVNKNQQYHKEREQPPRFAQPGTFEYEYAMRWKALMEMEKQQYEMVDRNMKEA

Parental  REKLEAEMEDAYHEHQANLLRQDLLRRQEELRRMEELHSQEMQKRKELQLRQEEERRRREEEMLRKREME
          .EKLEAEME.A.HEHQ..L.RQDLLRRQEELRRMEELH.QE.QKRK...LRQEEERRRREEEM...R...
Retrocopy QEKLEAEMEAARHEHQVMLMRQDLLRRQEELRRMEELHNQEVQKRKQAELRQEEERRRREEEM---RLRN

Parental  EQMRRQREENYRMGGFMDREREMRMNSGG-AMGLGDMSFGAAGQKFPMGGLGFEGQQGMGSSPGN
          E.M.....E..R......RE...RM..G...M........AA.......G...E....M.S.PGN
Retrocopy EEMMKRQQEGFRANFSENREQDLRMHMGSHGMPMNRNNLAAAAGAAAAPGMASENAAIM-SGPGN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Takifugu rubripes was not studied using RNA-Seq expression data.

ChIP-Seq

Takifugu rubripes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_trub_8 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_8 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_8 has 0 orthologous retrocopies within teleost group .

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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,