RetrogeneDB ID: retro_tnig_32

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: Un_random:31136503..31137393(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: sfpq
• Ensembl ID: ENSTNIG00000011331
• Aliases: None
• Description: splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated) [Source:ZFIN;Acc:ZDB-GENE-040426-2452]

Sequence

>retro_tnig_32
GGTCCCCAGCAAAATCATGGTTTCAATCGTTCAGGAGAGCAGAAAAAACCTGGGGGAACAAACACCAATGGGCAGCCACC
CGAGCTCAGCGAGCAGAACTCCAACGAGGCCTTAACCCTGGACCTGCAAAGCTTCAGGAAGCCCGGTGAGAAAACCTTCA
CGCAGCGAAGCCGGCTGTTTGTTGGAAACCTCCCAGCCGGAGTTATAGAGGAGGATCTGGAGAGACTGTTTGCCAAATAC
GGCAAAGCAAGTGAGATTTTTATCAATAAAGAGCGAGGTTTCGGCTTTATTCGCCTGGAGACTAGGATCATAGCAGAGAT
CGCCAGAGCAGAGCTGGATGATACACCATTCCGTGGCAGACCCATTCGAGTAAGGTTTGCCACGCACGGTGCTGCGTTGA
CTGTGAAAAATCTGCCAGAGTTTGTGTCTAATGAATTGCTGGAGGAGGCCTTCGCTGTCTTTGGTCAAATCGAAAGAGCT
GTTGTTGTCGTGGATGATCGAGGAAGGCCCACGGGGAAGGGGATATTGTGGAGTACACATCTAAACCAGCGGCGAGGAAA
GCTCTAGACAAGTGTAGTGATGGTTCCTATCTCCTCACAGCATTCCCACGACCTGTTACAGTGGAACCTATGGAGCAACT
TGACGATGATGAGGGACTACCAGAAAAACTTGTAAACAAAAACCAGCAGTATCATAAAGAACGTGAACAACCACCACGAT
TTGCACAGCCTGGTAGTTTTGAGTATGAATATGCAATGCGTTGGAAGGCTCTGATGGAGATGGAGAAGCAGCAGTATGAC
ATGGTGGATCGCAATATGAAGGAAGCTCAGGAGAAGCTGGAGGCTGAGATGGAGGCAGCCCGACATGAGCATCAAGTGAT
GCTCATGAAA

Alignment

ORF - retro_tnig_32 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.07 %
• Parental protein coverage: 50.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPQQGQRLGPQQNQRS-GQQQVHKATPITIKREDGQEFKATLSMLLKPGEKRYTQRCRLFIGNLPNDITE
          GPQQ.........Q...G........P..............L....KPGEK..TQR.RLF.GNLP....E
Retrocopy GPQQNHGFNRSGEQKKPGGTNTNGQPPELSEQNSNEALTLDLQSFRKPGEKTFTQRSRLFVGNLPAGVIE

Parental  DAFKKLFAKYGEPSEVFINKGKGFGFIRLESRALAEIAKAELDDTPMKGRPLRVRFATHSAALSVKNLSP
          .....LFAKYG..SE.FINK..GFGFIRLE.R..AEIA.AELDDTP..GRP.RVRFATH.AAL.VKNL..
Retrocopy EDLERLFAKYGKASEIFINKERGFGFIRLETRIIAEIARAELDDTPFRGRPIRVRFATHGAALTVKNLPE

Parental  FVSNELLEEAFSQFGMVERAVVIVDDRGRST-GKG-IVEFASKPAARKALDRCNEGVFLLTSSPRPVVVE
          FVSNELLEEAF..FG..ERAVV.VDDRGR.T.G.G.IVE..SKPAARKALD.C..G..LLT..PRPV.VE
Retrocopy FVSNELLEEAFAVFGQIERAVVVVDDRGRPT<GEGDIVEYTSKPAARKALDKCSDGSYLLTAFPRPVTVE

Parental  PLEQFDDEDGLPEKLAQKNPRYQAEREEPPRFARPGTFEFEYAKRWKSLDEMEKQQRQQVEKNMQEAREK
          P.EQ.DD..GLPEKL..KN..Y..ERE.PPRFA.PG.FE.EYA.RWK.L.EMEKQQ...V..NM.EA.EK
Retrocopy PMEQLDDDEGLPEKLVNKNQQYHKEREQPPRFAQPGSFEYEYAMRWKALMEMEKQQYDMVDRNMKEAQEK

Parental  LEAEMEDAFHEHQANLLR
          LEAEME.A.HEHQ..L..
Retrocopy LEAEMEAARHEHQVMLMK

Legend:

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

Expression

RNA-Seq

Tetraodon nigroviridis was not studied using RNA-Seq expression data.

ChIP-Seq

Tetraodon nigroviridis was not studied using ChIP-Seq data.

EST

Tetraodon nigroviridis was not studied using EST data.

TSS

Tetraodon nigroviridis was not studied using FANTOM5 data.

Lab

retro_tnig_32 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_32 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,