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 summary:
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]


Retrocopy-Parental alignment summary:






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

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:

ParentalGPQQGQRLGPQQNQRS-GQQQVHKATPITIKREDGQEFKATLSMLLKPGEKRYTQRCRLFIGNLPNDITE
GPQQ.........Q...G........P..............L....KPGEK..TQR.RLF.GNLP....E
RetrocopyGPQQNHGFNRSGEQKKPGGTNTNGQPPELSEQNSNEALTLDLQSFRKPGEKTFTQRSRLFVGNLPAGVIE
ParentalDAFKKLFAKYGEPSEVFINKGKGFGFIRLESRALAEIAKAELDDTPMKGRPLRVRFATHSAALSVKNLSP
.....LFAKYG..SE.FINK..GFGFIRLE.R..AEIA.AELDDTP..GRP.RVRFATH.AAL.VKNL..
RetrocopyEDLERLFAKYGKASEIFINKERGFGFIRLETRIIAEIARAELDDTPFRGRPIRVRFATHGAALTVKNLPE
ParentalFVSNELLEEAFSQFGMVERAVVIVDDRGRST-GKG-IVEFASKPAARKALDRCNEGVFLLTSSPRPVVVE
FVSNELLEEAF..FG..ERAVV.VDDRGR.T.G.G.IVE..SKPAARKALD.C..G..LLT..PRPV.VE
RetrocopyFVSNELLEEAFAVFGQIERAVVVVDDRGRPT<GEGDIVEYTSKPAARKALDKCSDGSYLLTAFPRPVTVE
ParentalPLEQFDDEDGLPEKLAQKNPRYQAEREEPPRFARPGTFEFEYAKRWKSLDEMEKQQRQQVEKNMQEAREK
P.EQ.DD..GLPEKL..KN..Y..ERE.PPRFA.PG.FE.EYA.RWK.L.EMEKQQ...V..NM.EA.EK
RetrocopyPMEQLDDDEGLPEKLVNKNQQYHKEREQPPRFAQPGSFEYEYAMRWKALMEMEKQQYDMVDRNMKEAQEK
ParentalLEAEMEDAFHEHQANLLR
LEAEME.A.HEHQ..L..
RetrocopyLEAEMEAARHEHQVMLMK

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






Tetraodon nigroviridis was not studied using RNA-Seq expression data.
Tetraodon nigroviridis was not studied using ChIP-Seq data.
Tetraodon nigroviridis was not studied using EST data.
Tetraodon nigroviridis was not studied using FANTOM5 data.
retro_tnig_32 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_tnig_32 has 0 orthologous retrocopies within teleost group .


Parental genes homology:
Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000035951 retrocopy
Callithrix jacchus ENSCJAG000000014314 retrocopies
Felis catus ENSFCAG000000312871 retrocopy
Gasterosteus aculeatus ENSGACG000000020341 retrocopy
Gadus morhua ENSGMOG000000119501 retrocopy
Macropus eugenii ENSMEUG000000140821 retrocopy
Oryctolagus cuniculus ENSOCUG000000018771 retrocopy
Oreochromis niloticus ENSONIG000000177371 retrocopy
Sarcophilus harrisii ENSSHAG000000161071 retrocopy
Tetraodon nigroviridis ENSTNIG00000011331 1 retrocopy
retro_tnig_32 ,
Takifugu rubripes ENSTRUG000000037831 retrocopy
Drosophila melanogaster FBgn00042271 retrocopy



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