RetrogeneDB ID:

retro_sscr_1168

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:X:86937135..86937494(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL35
Ensembl ID:ENSSSCG00000005595
Aliases:None
Description:Sus scrofa ribosomal protein L35 (RPL35), mRNA. [Source:RefSeq mRNA;Acc:NM_214326]


Retrocopy-Parental alignment summary:






>retro_sscr_1168
ATGGCTTAGGTTAAGGCTTGAGATCTTTGAGGTAAGAAGATAGAGCTGCAGAAACAGCTGGATGACTTGAAGGTGGAACT
GTCCTAGCTAGGCATCACCAAGGTGACAGGTGGTACAGCATCTAAGCTCTCCAAGTTCCTAGTTGATTGCAAATCTATCA
CCTAAGTTCTCACTGTCATTAACCAGACTCGGAAAGAGAACCCCAGGAAATTCCACAAGGGCAAGAAGTACAAGCCTCTG
GATTTGCAGCCCAAGAAACCACATGCTACAGGTTCAACAAGCATAAGGAGAAGTTGAGGACCAAGAAGTGGCAGCAGAAG
AAAGAGTTGTACCCACTGCTGAAGTTTGTAGTCAAGGCC

ORF - retro_sscr_1168 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.13 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 5
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMAKIKARDLRGKKKEELLKQLEDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTVINQTQKENLR
MA..KA.DL.GKK.E.L.KQL.DLKVELS.L...KVTGG.ASKLSK..V..KSI..VLTVINQT.KEN.R
RetrocopyMA*VKA*DL*GKKIE-LQKQLDDLKVELS*LGITKVTGGTASKLSKFLVDCKSIT*VLTVINQTRKENPR
ParentalKFYKGKKYKPLDLRPKK-TRAMRRRLNKHEENLKTKKQQRKERLYPLRKFAVKA
KF.KGKKYKPLDL.PKK.T...R....K.....K.K.QQ.KE.LYPL.KF.VKA
RetrocopyKFHKGKKYKPLDLQPKK<TTCYRFNKHKEKLRTK-KWQQKKE-LYPLLKFVVKA

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP014902_placenta 0 .00 RPM 228 .70 RPM
SRP014902_testis 0 .00 RPM 744 .01 RPM
SRP018288_heart 0 .00 RPM 201 .93 RPM
SRP018288_kidney 0 .00 RPM 260 .15 RPM
SRP018288_liver 0 .00 RPM 220 .84 RPM
SRP018288_lung 0 .00 RPM 253 .04 RPM
SRP018856_adipose 0 .00 RPM 1406 .72 RPM
SRP035408_brain 0 .00 RPM 723 .34 RPM
SRP035408_liver 0 .00 RPM 544 .87 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_sscr_1168 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_1168 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_1168 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Equus caballus retro_ecab_1083
Parental genes homology:
Parental genes homology involve 29 parental genes, and 145 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001653712 retrocopies
retro_amel_1010, retro_amel_1180, retro_amel_1341, retro_amel_1686, retro_amel_1746, retro_amel_1844, retro_amel_1887, retro_amel_351, retro_amel_584, retro_amel_819, retro_amel_893, retro_amel_94,
Bos taurus ENSBTAG000000032053 retrocopies
retro_btau_1060, retro_btau_1340, retro_btau_185,
Canis familiaris ENSCAFG000000202127 retrocopies
retro_cfam_1566, retro_cfam_1635, retro_cfam_2180, retro_cfam_294, retro_cfam_529, retro_cfam_738, retro_cfam_995,
Callithrix jacchus ENSCJAG000000067245 retrocopies
retro_cjac_1074, retro_cjac_1308, retro_cjac_1377, retro_cjac_2458, retro_cjac_387,
Cavia porcellus ENSCPOG000000228111 retrocopy
retro_cpor_414,
Equus caballus ENSECAG000000093893 retrocopies
retro_ecab_1083, retro_ecab_115, retro_ecab_813,
Erinaceus europaeus ENSEEUG000000126968 retrocopies
retro_eeur_144, retro_eeur_217, retro_eeur_225, retro_eeur_251, retro_eeur_319, retro_eeur_487, retro_eeur_533, retro_eeur_56,
Echinops telfairi ENSETEG0000000087610 retrocopies
retro_etel_1013, retro_etel_1267, retro_etel_1383, retro_etel_1556, retro_etel_1848, retro_etel_1931, retro_etel_303, retro_etel_637, retro_etel_747, retro_etel_942,
Felis catus ENSFCAG000000303885 retrocopies
retro_fcat_1129, retro_fcat_1790, retro_fcat_1954, retro_fcat_397, retro_fcat_782,
Homo sapiens ENSG000001369426 retrocopies
retro_hsap_1233, retro_hsap_326, retro_hsap_3579, retro_hsap_3832, retro_hsap_3867, retro_hsap_4026,
Gorilla gorilla ENSGGOG000000041113 retrocopies
retro_ggor_2581, retro_ggor_351, retro_ggor_966,
Loxodonta africana ENSLAFG000000100313 retrocopies
retro_lafr_128, retro_lafr_300, retro_lafr_642,
Microcebus murinus ENSMICG000000029222 retrocopies
retro_mmur_1502, retro_mmur_215,
Myotis lucifugus ENSMLUG000000293233 retrocopies
retro_mluc_1495, retro_mluc_2392, retro_mluc_969,
Macaca mulatta ENSMMUG000000052605 retrocopies
retro_mmul_1304, retro_mmul_156, retro_mmul_1623, retro_mmul_1912, retro_mmul_265,
Monodelphis domestica ENSMODG000000197531 retrocopy
retro_mdom_1039,
Mustela putorius furoENSMPUG000000139505 retrocopies
retro_mputfur_1136, retro_mputfur_1348, retro_mputfur_1478, retro_mputfur_1484, retro_mputfur_425,
Mus musculus ENSMUSG000000629971 retrocopy
retro_mmus_236,
Nomascus leucogenys ENSNLEG000000173037 retrocopies
retro_nleu_1153, retro_nleu_1770, retro_nleu_1850, retro_nleu_1921, retro_nleu_2104, retro_nleu_2836, retro_nleu_953,
Ornithorhynchus anatinus ENSOANG000000116121 retrocopy
retro_oana_56,
Oryctolagus cuniculus ENSOCUG000000029964 retrocopies
retro_ocun_200, retro_ocun_238, retro_ocun_451, retro_ocun_791,
Otolemur garnettii ENSOGAG000000085137 retrocopies
retro_ogar_1265, retro_ogar_1271, retro_ogar_1828, retro_ogar_2005, retro_ogar_2253, retro_ogar_2610, retro_ogar_2903,
Ochotona princeps ENSOPRG000000004069 retrocopies
retro_opri_1077, retro_opri_1134, retro_opri_244, retro_opri_273, retro_opri_339, retro_opri_473, retro_opri_565, retro_opri_628, retro_opri_650,
Pongo abelii ENSPPYG000000196037 retrocopies
retro_pabe_1026, retro_pabe_165, retro_pabe_1718, retro_pabe_2948, retro_pabe_3064, retro_pabe_3303, retro_pabe_3304,
Pan troglodytes ENSPTRG000000213616 retrocopies
retro_ptro_2426, retro_ptro_2609, retro_ptro_262, retro_ptro_2635, retro_ptro_2730, retro_ptro_846,
Rattus norvegicus ENSRNOG0000001427214 retrocopies
retro_rnor_1254, retro_rnor_126, retro_rnor_147, retro_rnor_1473, retro_rnor_1509, retro_rnor_1768, retro_rnor_1957, retro_rnor_205, retro_rnor_2183, retro_rnor_233, retro_rnor_2618, retro_rnor_2681, retro_rnor_2719, retro_rnor_451,
Sarcophilus harrisii ENSSHAG000000047561 retrocopy
retro_shar_775,
Sus scrofa ENSSSCG00000005595 5 retrocopies
retro_sscr_1168 , retro_sscr_214, retro_sscr_553, retro_sscr_679, retro_sscr_905,
Ictidomys tridecemlineatus ENSSTOG000000079011 retrocopy
retro_itri_1735,


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