RetrogeneDB ID:

retro_ttru_1337

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:scaffold_110858:374515..375098(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:APOOL
Ensembl ID:ENSTTRG00000000429
Aliases:None
Description:apolipoprotein O-like [Source:HGNC Symbol;Acc:24009]


Retrocopy-Parental alignment summary:






>retro_ttru_1337
ATGGGAAAGGAGACAACCATGCCAGCAGGTCTGATATGTGCATCTGTAAGAGTGCGTGTGGCCAAAGAAGAGGAGTCCAA
GGAGCAGCTAGTGAAACCAAAGCAGCTCCCCATATATACTGCGCCACCTCTCCAGTCTAAATATGTTGAAGAACAGCCCG
GTGACTTACAAATGGGCTTTGCATCCATTCGCACTACAACTGGTCATTATATTGGCTGGTGCAAGGATGTTTATGTCTTT
GTGAAAAATGGGATAATGGATACAGCACAATTTGGAAAAGATGCATATGTCTATCTGAAGAATCCACCTCGAGACTTTCT
TCCGAAAATTGGAGTGATTACAGTTTCAGGATTGGCAGCCTTCATTTCAGCGAGAAAAGGTTCTAGGTTTAAGAGAATTG
CTTATCCACTGGGACTGGCCACTTTAGGAGCAACTGTTCTCTACCCTGTTCAATCAGTAATGATTGCAAAGGTAACTGGG
AAAAAGGCATGTGCTATAAGCCAGCAAATTTATGAAGCAGTTCAATCATTGTGGACAAAAAACAACAAAAAGGAGTCATT
TCCTGAACCAAAAGAAAAAGCTA

ORF - retro_ttru_1337 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.13 %
Parental protein coverage: 72.39 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMGKLTTMPAALICASISVHAAKEEESRKHLVKPEQLPIYTAPPLQSKYVDEQPGHLQMGFASIRTTTGRY
MGK.TTMPA.LICAS..V..AKEEES...LVKP.QLPIYTAPPLQSKYV.EQPG.LQMGFASIRTTTG.Y
RetrocopyMGKETTMPAGLICASVRVRVAKEEESKEQLVKPKQLPIYTAPPLQSKYVEEQPGDLQMGFASIRTTTGHY
ParentalIGWCKGVYVFMKYGIMDTVQFGKDAYVYLKNPPRDFLPKIGVITVSGLAGFISARKGSRFKRIAYPLGLA
IGWCK.VYVF.K.GIMDT.QFGKDAYVYLKNPPRDFLPKIGVITVSGLA.FISARKGSRFKRIAYPLGLA
RetrocopyIGWCKDVYVFVKNGIMDTAQFGKDAYVYLKNPPRDFLPKIGVITVSGLAAFISARKGSRFKRIAYPLGLA
ParentalTLGATVCYPVQSVIIAKVS-GKRHMLQASRFMKRLNHCGQKTTKKSHFLNLKKKL
TLGATV.YPVQSV.IAKV..GKRH.L.AS.FMK..NHCGQKTTK.SHFLN.KKKL
RetrocopyTLGATVLYPVQSVMIAKVT>GKRHVL*ASKFMKQFNHCGQKTTKRSHFLNQKKKL

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_1337 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_1337 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 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000008291 retrocopy
retro_amel_1035,
Canis familiaris ENSCAFG000000173831 retrocopy
retro_cfam_1490,
Callithrix jacchus ENSCJAG000000082492 retrocopies
retro_cjac_1783, retro_cjac_2464,
Dipodomys ordii ENSDORG000000110451 retrocopy
retro_dord_373,
Equus caballus ENSECAG000000092291 retrocopy
retro_ecab_577,
Homo sapiens ENSG000001550081 retrocopy
retro_hsap_3253,
Gorilla gorilla ENSGGOG000000163291 retrocopy
retro_ggor_2213,
Loxodonta africana ENSLAFG000000088441 retrocopy
retro_lafr_1035,
Microcebus murinus ENSMICG000000158441 retrocopy
retro_mmur_1511,
Myotis lucifugus ENSMLUG000000113841 retrocopy
retro_mluc_1364,
Macaca mulatta ENSMMUG000000043351 retrocopy
retro_mmul_2045,
Mustela putorius furoENSMPUG000000018993 retrocopies
retro_mputfur_606, retro_mputfur_734, retro_mputfur_874,
Nomascus leucogenys ENSNLEG000000026341 retrocopy
retro_nleu_1702,
Pongo abelii ENSPPYG000000205161 retrocopy
retro_pabe_2697,
Pan troglodytes ENSPTRG000000220671 retrocopy
retro_ptro_2200,
Sus scrofa ENSSSCG000000124591 retrocopy
retro_sscr_610,
Tupaia belangeri ENSTBEG000000101475 retrocopies
retro_tbel_2037, retro_tbel_2609, retro_tbel_2840, retro_tbel_3361, retro_tbel_3737,
Tursiops truncatus ENSTTRG00000000429 1 retrocopy
retro_ttru_1337 ,


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