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






RNA-Seq - click to see more details

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tursiops truncatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ttru_246 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

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
retro_amel_107, retro_amel_676,
Bos taurus ENSBTAG000000171253 retrocopies
retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris ENSCAFG000000030812 retrocopies
retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni ENSCHOG000000053273 retrocopies
retro_chof_1150, retro_chof_1182, retro_chof_1274,
Equus caballus ENSECAG000000093962 retrocopies
retro_ecab_2, retro_ecab_502,
Felis catus ENSFCAG000000152542 retrocopies
retro_fcat_116, retro_fcat_545,
Loxodonta africana ENSLAFG000000001513 retrocopies
retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus ENSMICG000000166331 retrocopy
retro_mmur_675,
Myotis lucifugus ENSMLUG000000120682 retrocopies
retro_mluc_228, retro_mluc_397,
Monodelphis domestica ENSMODG000000176572 retrocopies
retro_mdom_1090, retro_mdom_1805,
Mustela putorius furoENSMPUG000000144142 retrocopies
retro_mputfur_152, retro_mputfur_546,
Mus musculus ENSMUSG000000112577 retrocopies
retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Rattus norvegicus ENSRNOG000000156422 retrocopies
retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii ENSSHAG000000181391 retrocopy
retro_shar_823,
Sus scrofa ENSSSCG000000036603 retrocopies
retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus ENSTTRG000000021171 retrocopy
retro_ttru_715,
Tursiops truncatus ENSTTRG000000046892 retrocopies
retro_ttru_1050, retro_ttru_1812,
Tursiops truncatus ENSTTRG00000014340 2 retrocopies
retro_ttru_1117, retro_ttru_246 ,


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