RetrogeneDB ID:

retro_onil_28

Retrocopy
location
Organism:Tilapia (Oreochromis niloticus)
Coordinates:GL831360.1:963778..964432(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSONIG00000020975
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:eef1b2 (2 of 2)
Ensembl ID:ENSONIG00000017630
Aliases:None
Description:eukaryotic translation elongation factor 1 beta 2 [Source:ZFIN;Acc:ZDB-GENE-030131-7310]


Retrocopy-Parental alignment summary:






>retro_onil_28
TTTGGTGACGTGAGCACACAAGTGGGCCTCGAAGCTCTCAGTGATTTTCTGGCTGACAAAAGCTACATCGAGGGCTTTGT
GGCATCCCAGGCTGACATGATCGTGTTTGACGCCATCCCCTCTCCTCCCTCACCGACGCTCTGCCACCTCTGGCGCTGGT
ACAACCACATAAAGTCTTTCCAGACAGACAGAGCTCGTCTTCCATCAGCCAAGAGTCGGTATGTCCTCCCAGCTACTCCA
CCGGCCACGCCAAACGATGCCAGCGACGAGGAAGACATCGACCTTTTTGGGTCAGATGACGAGGCAGAGAGCGCAGAAGC
GGCCAGAATCAAGGAGCAGCGCCTCGCCGAGTATGCCGCCAAGAAATCCAAGAAGCCAGCTCTCGTCGCCAAGTCCTCCA
TCCTGCTTGACGTCAAGCCCTGGGACGACGAGACGGACATGTCCAAGCTGGAGGAGTGCGTCCGCAGCGTCAGCATGGAC
GGGCTGCTGTGGGGGCAGTCCAAGCTGGTGCCAGTGGGTTACGGCATCAAGAAGCTCCAGATAGGATGTGTGGTGGAGGA
CGATAAAGTGGGCACTGATATGTTGGAGGAAGCCATTACCGCCTTCGAGGAATATGTTCAGTCTGTGGATGTGGCTGCTT
TCAATAAGATTTGA

ORF - retro_onil_28 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.93 %
Parental protein coverage: 99.12 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalFGDLKSASGLKVLNDFLSDRSYIEGYVPSQADVAVFEAISAPPPADLCHALRWYNHIRSYQSEKSSLPGV
FGD.....GL..L.DFL.D.SYIEG.V.SQAD..VF.AI..PP...LCH..RWYNHI.S.Q.....LP..
RetrocopyFGDVSTQVGLEALSDFLADKSYIEGFVASQADMIVFDAIPSPPSPTLCHLWRWYNHIKSFQTDRARLPSA
ParentalKKPLGQYGPPGVADTTSGSAPTTAKDEDDDDIDLFGSDEEKEDAEATRLKEERLAAYAAKKAKKPAVIAK
K.....Y..P.....T...A......ED.D...LFGSD.E.E.AEA.R.KE.RLA.YAAKK.KKPA..AK
RetrocopyK---SRYVLPATPPATPNDA---SDEEDID---LFGSDDEAESAEAARIKEQRLAEYAAKKSKKPALVAK
ParentalSSILLDVKPWDDETDMAKLEECVRSIQMDGLVWGQSKLVPVGYGIKKLQINCVVEDDKVGTDILEEKITE
SSILLDVKPWDDETDM.KLEECVRS..MDGL.WGQSKLVPVGYGIKKLQI.CVVEDDKVGTD.LEE.IT.
RetrocopySSILLDVKPWDDETDMSKLEECVRSVSMDGLLWGQSKLVPVGYGIKKLQIGCVVEDDKVGTDMLEEAITA
ParentalFEDFVQSMDVAAFNKI
FE..VQS.DVAAFNKI
RetrocopyFEEYVQSVDVAAFNKI

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






RNA-Seq - click to see more details

Oreochromis niloticus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Oreochromis niloticus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_onil_28 retrocopy.

TSS - click to see more details

Oreochromis niloticus was not studied using FANTOM5 data.

Lab - click to see more details

retro_onil_28 was not experimentally validated.

Retrocopy orthology:
Oreochromis niloticus 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 29 parental genes, and 106 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000030151 retrocopy
retro_amel_427,
Bos taurus ENSBTAG000000219798 retrocopies
retro_btau_1127, retro_btau_1309, retro_btau_1786, retro_btau_366, retro_btau_367, retro_btau_450, retro_btau_512, retro_btau_792,
Canis familiaris ENSCAFG000000296351 retrocopy
retro_cfam_56,
Choloepus hoffmanni ENSCHOG000000138351 retrocopy
retro_chof_725,
Callithrix jacchus ENSCJAG000000058052 retrocopies
retro_cjac_176, retro_cjac_341,
Cavia porcellus ENSCPOG000000144964 retrocopies
retro_cpor_1116, retro_cpor_1381, retro_cpor_1407, retro_cpor_296,
Dipodomys ordii ENSDORG000000036692 retrocopies
retro_dord_510, retro_dord_592,
Felis catus ENSFCAG000000102391 retrocopy
retro_fcat_1735,
Homo sapiens ENSG000001149429 retrocopies
retro_hsap_1154, retro_hsap_1500, retro_hsap_2397, retro_hsap_2883, retro_hsap_3332, retro_hsap_3480, retro_hsap_3657, retro_hsap_3903, retro_hsap_4795,
Gorilla gorilla ENSGGOG000000070022 retrocopies
retro_ggor_134, retro_ggor_2000,
Macropus eugenii ENSMEUG000000026548 retrocopies
retro_meug_1418, retro_meug_1846, retro_meug_1917, retro_meug_240, retro_meug_241, retro_meug_52, retro_meug_775, retro_meug_949,
Microcebus murinus ENSMICG000000106073 retrocopies
retro_mmur_1067, retro_mmur_615, retro_mmur_78,
Myotis lucifugus ENSMLUG000000166028 retrocopies
retro_mluc_1035, retro_mluc_1068, retro_mluc_1104, retro_mluc_1167, retro_mluc_1542, retro_mluc_1578, retro_mluc_1681, retro_mluc_1857,
Macaca mulatta ENSMMUG000000010546 retrocopies
retro_mmul_1456, retro_mmul_1767, retro_mmul_1881, retro_mmul_2140, retro_mmul_894, retro_mmul_969,
Nomascus leucogenys ENSNLEG000000070988 retrocopies
retro_nleu_1220, retro_nleu_1676, retro_nleu_2078, retro_nleu_2107, retro_nleu_2521, retro_nleu_2630, retro_nleu_624, retro_nleu_834,
Oryctolagus cuniculus ENSOCUG000000098484 retrocopies
retro_ocun_1014, retro_ocun_1240, retro_ocun_544, retro_ocun_922,
Otolemur garnettii ENSOGAG000000112293 retrocopies
retro_ogar_2628, retro_ogar_616, retro_ogar_862,
Oreochromis niloticus ENSONIG00000017630 1 retrocopy
retro_onil_28 ,
Ochotona princeps ENSOPRG000000171633 retrocopies
retro_opri_1192, retro_opri_294, retro_opri_748,
Oryzias latipes ENSORLG000000185331 retrocopy
retro_olat_16,
Procavia capensis ENSPCAG000000133481 retrocopy
retro_pcap_154,
Pongo abelii ENSPPYG000000131077 retrocopies
retro_pabe_1251, retro_pabe_1656, retro_pabe_2163, retro_pabe_2389, retro_pabe_2419, retro_pabe_2746, retro_pabe_2876,
Pteropus vampyrus ENSPVAG000000173342 retrocopies
retro_pvam_1055, retro_pvam_56,
Sorex araneus ENSSARG000000015241 retrocopy
retro_sara_463,
Sarcophilus harrisii ENSSHAG000000178531 retrocopy
retro_shar_208,
Sus scrofa ENSSSCG000000161281 retrocopy
retro_sscr_766,
Ictidomys tridecemlineatus ENSSTOG000000054373 retrocopies
retro_itri_1263, retro_itri_813, retro_itri_873,
Tupaia belangeri ENSTBEG0000000565713 retrocopies
retro_tbel_161, retro_tbel_2046, retro_tbel_2094, retro_tbel_2298, retro_tbel_2700, retro_tbel_2776, retro_tbel_3143, retro_tbel_3541, retro_tbel_3542, retro_tbel_4050, retro_tbel_4073, retro_tbel_4205, retro_tbel_611,
Xiphophorus maculatus ENSXMAG000000060501 retrocopy
retro_xmac_21,


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