RetrogeneDB ID:

retro_ttru_246

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:GeneScaffold_168:153233..154477(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PABPC4
Ensembl ID:ENSTTRG00000014340
Aliases:None
Description:poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]


Retrocopy-Parental alignment summary:






>retro_ttru_246
GCCGTGGAAGAGATGAATGGAAAAGAAATCAGTGGGAAAGTCATTTTCGTCGGCCGTGCACAGAAGAAAGTGGAACAGCA
GGCCGAGTTAAAGCGAAAATTTGAACAGCTCAAACAGGAGAGAATTAGTTGCTATCAGGGGGTGAATCTCTAAATTAAGA
ACTTGGATGACACCATTGATGGTGAGAAGTTAAGGAAAAAATTCTCTCCTTTTGGATCAATCAGCAGTGCTAAGGTGATG
CTGGAGGATGGGAGAAGCAAAGGGTTTGCCTTTGTCTGCTTCTGATCCCCTGAAGAGGCAACCAAAGCAGTCACGGAGAT
GAACGGATGCATCGTGGGCTTCAAGCCACTGTATGTCGCCCTGGCCCAGAGAAAGGAAGAGAGAAAGGCTCAGCTGACCA
ACCAGTATATGCAGCGGGTGACCAGGATGAGAGCAGTCCCTGCCAATGCCATCTTAAATCATTTCCAGCAGCTGGGGGCT
ACTTTGTGCCAGCAGTTCCACAGGCCCAGGGAAGACCTCCGTATTACCTAACGAGTTAGCACAGATGAGGCCTAAGCCAC
GCTGCAGCAAGGTGGGAGACCTCAAAGCTTCCAAGGAATGCCAAGTGCTATACGCCAGTCTGGGCCTCGTCCAGCTCTTC
GCCATCTGGCTCCAACTGGTAATGCTCTGGCCTCTCACGGCCTCCCTACTACCGCTCAGAGAGTCGGATCTGAGTGCCCA
GACCGCTTGGCTATGGACTTTGGTGGGGCTGGTGCCGCCCAGCAAGGGCCGACTGACAGCTGCCAGTCTGGAGGTGTTCC
CACAGCTGGGCAGAACCTAGCGCCTCGTGCTGCTGTTGCTGCCGCTGCTGCTCGGGCTGTTGCACCTTACAAATACGCCT
CCAGTGTCCACAGCCCTCACCCTGCCATCCAGCCCCTGCAGGCACCCCAGCCTGTGGTCCATGTGCAGGGGCAGGAGCCG
CTGACCGCCTCCATGCTGGCCGCAGCACCCCCCCCCCCTGCCCCCAAGGAGCAGAAGCAGATGCTGGGTGAACGTTTGTT
CCTCCTCATCCAGACGATGCACTCAAACCTGGCCGGGAAGATTACGGGGATGCTGCTGGAGGTTGACAGCTCGGAGCTGC
TGCACGTGCTGGAGTCCCCGAGTCTCTCCGCTCCCACATGGATGAAGCTGTGGCGGTCCTACAGGCTCATCATGCCAAGA
AAGAAGGTGCCCAGAAGGTGGGCACTGTCGCTGCTGCTACCTCG

ORF - retro_ttru_246 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.78 %
Parental protein coverage: 74.59 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKFEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSP
AVEEMNGKEISGKVIFVGRAQKKVE.QAELKRKFEQLKQERIS.YQGVNL.IKNLDDTID.EKLRK.FSP
RetrocopyAVEEMNGKEISGKVIFVGRAQKKVEQQAELKRKFEQLKQERISCYQGVNL*IKNLDDTIDGEKLRKKFSP
ParentalFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRV
FGSI.SAKVMLEDGRSKGF.FVCF.SPEEATKAVTEMNG.IVG.KPLYVALAQRKEERKA.LTNQYMQRV
RetrocopyFGSISSAKVMLEDGRSKGFAFVCF*SPEEATKAVTEMNGCIVGFKPLYVALAQRKEERKAQLTNQYMQRV
ParentalAGMRALPANAI-LNQFQPAAGGYFVPAVPQAQGRPPYY-TPNQLAQMRPNPRW-QQGGRPQGFQGMPSAI
..MRA.PANAI.L..F.PAAGGYFVPAVPQAQGR.P.Y..PN.LAQMRP.PR..QQGGRPQ.FQGMPSAI
RetrocopyTRMRAVPANAI<LKSF-PAAGGYFVPAVPQAQGR-PPY<LPNELAQMRPKPRC<QQGGRPQSFQGMPSAI
ParentalRQSGPRPALRHLAPTGNAPASRGLPTTAQRVGSECPDRLAMDFGGAGAAQQGLTDSCQSGGVPTAVQSLA
RQSGPRPALRHLAPTGNA.AS.GLPTTAQRVGSECPDRLAMDFGGAGAAQQG.TDSCQSGGVPTA.Q.LA
RetrocopyRQSGPRPALRHLAPTGNALASHGLPTTAQRVGSECPDRLAMDFGGAGAAQQGPTDSCQSGGVPTAGQNLA
ParentalPRAAVATAAPRAVAPYKYASSVRSPHPAIQPLQAPQPAVHVQGQEP----LTASMLAAAPPQEQKQMLGE
PRAAVA.AA.RAVAPYKYASSV.SPHPAIQPLQAPQP.VHVQGQEP......A.........EQKQMLGE
RetrocopyPRAAVAAAAARAVAPYKYASSVHSPHPAIQPLQAPQPVVHVQGQEPLTASMLAAAXXXXXXKEQKQMLGE
ParentalRLFPLIQTMHSNLAGKITGMLLEIDNSELLHMLES-PESLRSKVDEAVAVLQAHHAKKEAAQKVGAVAAA
RLF.LIQTMHSNLAGKITGMLLE.D.SELLH.LES.PESLRS..DEAVAVLQAHHAKKE.AQKVG.VAAA
RetrocopyRLFLLIQTMHSNLAGKITGMLLEVDSSELLHVLES<PESLRSHMDEAVAVLQAHHAKKEGAQKVGTVAAA
ParentalTS
TS
RetrocopyTS

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






Tursiops truncatus was not studied using RNA-Seq expression data.
Tursiops truncatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ttru_246 retrocopy.
Tursiops truncatus was not studied using FANTOM5 data.
retro_ttru_246 was not experimentally validated.

Retrocopy orthology:
Tursiops truncatus 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.

Parental genes homology:
Parental genes homology involve 18 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000115352 retrocopies
Bos taurus ENSBTAG000000171253 retrocopies
Canis familiaris ENSCAFG000000030812 retrocopies
Choloepus hoffmanni ENSCHOG000000053273 retrocopies
Equus caballus ENSECAG000000093962 retrocopies
Felis catus ENSFCAG000000152542 retrocopies
Loxodonta africana ENSLAFG000000001513 retrocopies
Microcebus murinus ENSMICG000000166331 retrocopy
Myotis lucifugus ENSMLUG000000120682 retrocopies
Monodelphis domestica ENSMODG000000176572 retrocopies
Mustela putorius furoENSMPUG000000144142 retrocopies
Mus musculus ENSMUSG000000112577 retrocopies
Rattus norvegicus ENSRNOG000000156422 retrocopies
Sarcophilus harrisii ENSSHAG000000181391 retrocopy
Sus scrofa ENSSSCG000000036603 retrocopies
Tursiops truncatus ENSTTRG000000021171 retrocopy
Tursiops truncatus ENSTTRG000000046892 retrocopies
Tursiops truncatus ENSTTRG00000014340 2 retrocopies
retro_ttru_1117, retro_ttru_246 ,



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