RetrogeneDB ID:

retro_ttru_466

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:GeneScaffold_2381:111984..113131(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SSB
Ensembl ID:ENSTTRG00000002152
Aliases:None
Description:Sjogren syndrome antigen B (autoantigen La) [Source:HGNC Symbol;Acc:11316]


Retrocopy-Parental alignment summary:






>retro_ttru_466
ATGGCAGAAAATGGTGATAATGAAAAAATGGCTGCCCTGGAGGCCAAAATCTGTCATCAAATCGAGTATTATTTTGGTGA
CTTCAATTCGTCACGTGACAAATTTTTAAAGGAATAGATCAAACTGGATGAAGTCTGGGTATCTTTGGAGATAATGATAA
AATTTAATAGGTTAAACCGTCTAACAACAGACTTTAATGTAATAGTAGAAGCGTTGAGCAAATCAAAGGTGGAACTTATG
GAAAAAAGTGAAGATAAAACTAAAATTAGAAGATCTCCAAGCAAACCCCTCCCTGAAGTGACTGATGAGTATAAAAATGA
TGTAAAAAACAGGTCTGTTTATTTTAAAGGCTTCCCAATTGATGCAACCTTTGATGACATAAAATAATGGTTGTAAGATA
AAGGTCAGGTACTAAATATTCAGATGAGAAGAACATTGCACAAAGCATTTAAGGGATCAATATTTGCTGTATTTGATACC
ATTGAATCTGCTAAGAAGTTTGTCGAGACCCCTGGCCAGAAGTACAAAGACACAGACCTGCTAATACTTTTCAAGGAAGA
TTACTTTGCAAAAAACAATGAAGAAAGAAAGCAAAATAAAATCGAAGCTAAATTACGAGCTAAACAAGAGCAAGAAGAAA
AACAAAAGTTAGCAGAAAATGCTGAAATGAAATCTCTAGAAGAAAAGATTGGCTGCTTACTGCAAGTCTCGGGGGACTTA
GATGATCAGACGTGTAGAGAAGATTTGCATATCCTTTTCTCAAATCATGGTGAAATAAAATGGATAGACTTTGTCAGAGG
AGCCAAAGAGGGGATAATTCTGTTTAAAGAAAAAGCTAAGGAAGCACGGGATAAAGCAAAAGACACAAATAATGGTAACC
TACAATTAAGGAACAAAGGGGTCACCTGAGAAGTACTAGAAGGAGATGTGGAAAAAGAAGCATTGAAAAAAATAATAGAA
GATCAACAAGAATCCCTAAACAAATGGAAGTCAAAAGGTCTCAGATTTAAAGGAAAAGGAAAGGGAAATAAAGCTGCCCA
GATTGCGTCTGCTAAAGGAAAAGTAGTTTCAGGGCAAGAAAACTAAATTTGACAGTGATGATGAACACGATGAAAATGGT
GCATCTAGACCAGTAAAAAGAGCAAGA

ORF - retro_ttru_466 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.95 %
Parental protein coverage: 94.32 %
Number of stop codons detected: 4
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMAENGDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVE
MAENGDNEKMAALEAKICHQIEYYFGDFN..RDKFLKE.IKLDE.WV.LEIMIKFNRLNRLTTDFNVIVE
RetrocopyMAENGDNEKMAALEAKICHQIEYYFGDFNSSRDKFLKE*IKLDEVWVSLEIMIKFNRLNRLTTDFNVIVE
ParentalALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPIDATLDDIKEWLEDKGQVLNI
ALSKSK.ELME.SEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVY.KGFPIDAT.DDIK.WL.DKGQVLNI
RetrocopyALSKSKVELMEKSEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYFKGFPIDATFDDIK*WL*DKGQVLNI
ParentalQMRRTLHKAFKGSIFAVFDTIESAKKFFETTGQKYKDTDLLILFKEDYFAKKNEERKQNKIEAKLRA-QE
QMRRTLHKAFKGSIFAVFDTIESAKKF.ET.GQKYKDTDLLILFKEDYFAK.NEERKQNKIEAKLRA.QE
RetrocopyQMRRTLHKAFKGSIFAVFDTIESAKKFVETPGQKYKDTDLLILFKEDYFAKNNEERKQNKIEAKLRAKQE
ParentalQEEKQKLAENAEMKSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAK
QEEKQKLAENAEMKSLEEKIGCLL..SGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAK
RetrocopyQEEKQKLAENAEMKSLEEKIGCLLQVSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAK
ParentalEALDKAKDANNGNLQLRNKEVTWEVLEGDVEKEALKKIIEDQQESLNKWKSKGRRFKGKGKGNKAAQIGS
EA.DKAKD.NNGNLQLRNK.VT.EVLEGDVEKEALKKIIEDQQESLNKWKSKG.RFKGKGKGNKAAQI.S
RetrocopyEARDKAKDTNNGNLQLRNKGVT*EVLEGDVEKEALKKIIEDQQESLNKWKSKGLRFKGKGKGNKAAQIAS
ParentalAKGKV-QFQGKK-TKFDSDDEHDENDASRPEKRAR
AKGKV..F...K.TKFDSDDEHDEN.ASRP.KRAR
RetrocopyAKGKV<SFRARK<TKFDSDDEHDENGASRPVKRAR

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_466 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_466 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 38 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000077635 retrocopies
retro_chof_1125, retro_chof_1292, retro_chof_1380, retro_chof_185, retro_chof_2593,
Dasypus novemcinctus ENSDNOG000000134501 retrocopy
retro_dnov_2038,
Echinops telfairi ENSETEG000000046141 retrocopy
retro_etel_2056,
Homo sapiens ENSG000001383851 retrocopy
retro_hsap_448,
Gorilla gorilla ENSGGOG000000115073 retrocopies
retro_ggor_2914, retro_ggor_434, retro_ggor_791,
Gorilla gorilla ENSGGOG000000234714 retrocopies
retro_ggor_2834, retro_ggor_2915, retro_ggor_433, retro_ggor_792,
Loxodonta africana ENSLAFG000000008673 retrocopies
retro_lafr_698, retro_lafr_745, retro_lafr_982,
Macropus eugenii ENSMEUG000000016501 retrocopy
retro_meug_1908,
Myotis lucifugus ENSMLUG000000163161 retrocopy
retro_mluc_2493,
Macaca mulatta ENSMMUG000000230512 retrocopies
retro_mmul_1153, retro_mmul_529,
Monodelphis domestica ENSMODG000000082271 retrocopy
retro_mdom_1080,
Nomascus leucogenys ENSNLEG000000049583 retrocopies
retro_nleu_1039, retro_nleu_177, retro_nleu_3011,
Otolemur garnettii ENSOGAG000000297681 retrocopy
retro_ogar_1642,
Pongo abelii ENSPPYG000000129193 retrocopies
retro_pabe_3408, retro_pabe_3641, retro_pabe_424,
Pan troglodytes ENSPTRG000000126201 retrocopy
retro_ptro_2509,
Rattus norvegicus ENSRNOG000000079981 retrocopy
retro_rnor_405,
Tupaia belangeri ENSTBEG000000090564 retrocopies
retro_tbel_1065, retro_tbel_1269, retro_tbel_3318, retro_tbel_4012,
Tursiops truncatus ENSTTRG00000002152 2 retrocopies
retro_ttru_1926, retro_ttru_466 ,


Copyright © RetrogeneDB 2014-2017