RetrogeneDB ID: retro_gacu_13

Retrocopy location

• Organism: Stickleback (Gasterosteus aculeatus)
• Coordinates: groupXIII:13224045..13225368(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGACG00000011824
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: sfpq
• Ensembl ID: ENSGACG00000002034
• Aliases: None
• Description: splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated) [Source:ZFIN;Acc:ZDB-GENE-040426-2452]

Sequence

>retro_gacu_13
ATGCAAGGAAACCGAGGCCCACAGCAGAACCACGGGCCGAACCGCCCGGGCGATCAGAAAAAACCCGGAGGAACAAACGC
CAACGGCCAGCAGCCGCAGCCCAGCGAGCAGAACAATCCCAACGAGGCCTTAACCCTGGATCTGCAGAGCTTCAGGAAGC
CCGGGGAGAAGACCTTCACCCAACGCAGCAGGTTATTTGTTGGAAACTTGCCGACCGGAGTTAACGAGGAAGATCTCGAG
AAGCTCTTCAACAAGTATGGCAAGGCCAGTGAAATCTTCATTAACAAAGAAAGAGGTTTCGGCTTCATTCGGCTGGAGAC
CAGGATCATAGCAGAAATCGCCAGAGCCGAGCTGGACGATGCTCCGTTCAGAGGCAGGCCCATACGGGTGAGGTTCGCGA
CACACGGCGCTGCTTTAACTGTGAAGAACTTACCTGATTTTGTGTCCAACGAGCTACTGGAGGAGGCCTTCGGCGTCTTC
GGGCAGATAGAAAGAGCCGTGGTCATAGTGGATGATCGAGGGAGGCCCACGGGGAAGGGAATAGTGGAGTACACCTCGAA
GCCGGCTGCAAGAAAGGCTTTGGATAAGTGCAGCGATGGTGCCTATCTCCTCACGGCCTTTCCTCGACCCATCACGGTGG
AACCTATGGAACAGCTCGACGAAGAGGAGGGACTCTCAGAAAAAATCATAAACAAAAACCAGCAGTATCACAAGGAGCGC
GAGCAGCCGCCGCGTTTCGCCCAGGCGGGCTCCTTCGAGTTTGAGTACGCCATGCGTTGGAAGGCCCTGATGGAGATGGA
GAAGCAGCAGTACGACATGGTGGACCGCAACATGAAGGAGGCGCAGGAGAAGCTGGAGGCTGAGATGGAGGCAGCTCGAC
ACGAGCATCAAGTGATGCTGATGAGACAGGACCTGCTGAGGCGGCAGGAGGAGCTGCGGAGGATGGAGGAGCTCCACAGC
CAGGAGGTGCAGAAGAGGAAACAGGCCGAGATCCGGCAGGAGGAGGAACGCCGGAGGCGGGAGGAGGAGATGAGGATGCG
CAACGAGGAGATGCTGAAGAGGCAGCAGGAGGGCTTCAGAGGCAACTTCGCTGAGAATAGGGAGCAAGACATGAGGATGC
ATATGGCCAATCACGGGATGAACAGAAACTCGCTGGGCGGCAATGCCGGTCCTGCCGGTGCTCCCGGCATGGCCGCCGAG
AATGCGCCGATGATGCCAGGGCCAGGTAACAACAACAACATGCCCGGAGGAGGCCAGGCTGGCTTCCCTAGAGGCCTCCC
TGGACCTGGAGACTATGGACCTAATAAGCAACGCAGATTTTGA

Alignment

ORF - retro_gacu_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.02 %
• Parental protein coverage: 60.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PQQ--GP-KPGPHQGQKTGPHQGNETPASDGSQDKQAFKATLSMLLKPGEKTYTQRCRLFIGNLPNDITE
          PQQ..GP..PG...........G.....S.......A....L....KPGEKT.TQR.RLF.GNLP....E
Retrocopy PQQNHGPNRPGDQKKPGGTNANGQQPQPSEQNNPNEALTLDLQSFRKPGEKTFTQRSRLFVGNLPTGVNE

Parental  EDFKKLFAKYGEPSEVFINKSKGFGFIRLESRALAEIAKAELDDTPMKSRPLRVRFATHSAALSVKNLSP
          ED..KLF.KYG..SE.FINK..GFGFIRLE.R..AEIA.AELDD.P...RP.RVRFATH.AAL.VKNL..
Retrocopy EDLEKLFNKYGKASEIFINKERGFGFIRLETRIIAEIARAELDDAPFRGRPIRVRFATHGAALTVKNLPD

Parental  FVSNELLEEAFAQFGMVERSIVIVDDRGRSTGRGIVEFASKPAARKALDRCNEGVFLLTTSPRPVVVEPL
          FVSNELLEEAF..FG..ER..VIVDDRGR.TG.GIVE..SKPAARKALD.C..G..LLT..PRP..VEP.
Retrocopy FVSNELLEEAFGVFGQIERAVVIVDDRGRPTGKGIVEYTSKPAARKALDKCSDGAYLLTAFPRPITVEPM

Parental  EQFDDEDGLPEKLAQKNPRYQAEREEPPRFARPGTFEYEYSKRWKSLDDMEKQQRQQVEKNMREAREKLE
          EQ.D.E.GL.EK...KN..Y..ERE.PPRFA..G.FE.EY..RWK.L..MEKQQ...V..NM.EA.EKLE
Retrocopy EQLDEEEGLSEKIINKNQQYHKEREQPPRFAQAGSFEFEYAMRWKALMEMEKQQYDMVDRNMKEAQEKLE

Parental  SEMEDAFHEHQANLLRQDLLRRQEELRRMEEVHSQEMQKRKEMQIRQEEERRRREEEMIRKRDMEEQMRR
          .EME.A.HEHQ..L.RQDLLRRQEELRRMEE.HSQE.QKRK...IRQEEERRRREEEM...R...E.M..
Retrocopy AEMEAARHEHQVMLMRQDLLRRQEELRRMEELHSQEVQKRKQAEIRQEEERRRREEEM---RMRNEEMLK

Parental  QREENYRMGNYMDQRDREMRMN
          ...E..R.GN....R...MRM.
Retrocopy RQQEGFR-GNFAENREQDMRMH

Legend:

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

Expression

RNA-Seq

Gasterosteus aculeatus was not studied using RNA-Seq expression data.

ChIP-Seq

Gasterosteus aculeatus was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_gacu_13 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CD494960	13223951	13224648	99.6	694	3	691
DT996500	13223940	13224586	97.4	632	14	617

TSS

Gasterosteus aculeatus was not studied using FANTOM5 data.

Lab

retro_gacu_13 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_gacu_13 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,