RetrogeneDB ID:

retro_itri_368

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393286.1:8583960..8584746(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS4X
Ensembl ID:ENSSTOG00000028692
Aliases:None
Description:ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]


Retrocopy-Parental alignment summary:






>retro_itri_368
GCTCATGGTCCCAAGAAGCATCTGAAGTGGGTAGCAGCTCTAAAGCATGGGCGAATGGGTAAATTGGATAGTATATCTGC
TCCTTGTCCATCCACTGGTCCCCACAAGCTGAGAGAATGTCTTCCTCTCACCATTTTTCTAAGGAACAGACTCAACTATG
CCCTGACCGGAGATGAAGTAAAAAACATTTGCATGCAGCACTTCATTAAAATTGATGGCAAAGTCTGAACTGATATAACC
TACCCCACTGGTTTTATGAATGTCATCAGCATTCATACAGCTGGAGAGAATTTCCATCTGATCTGTGACACCAAAGGTCA
TTTTTCTGTTCATTGCATTACACCTGAGGAAGCCAAGTCCAAGTTGGGCAACGTGAGAAAGATCTTTGTGGGCACAAAAG
GAATCCCTCATCACGGTGACTCATAATTCTCAAATGATTTGCTACCCTGATCCTCTAGTCAAGATGAATGACACAATTCA
GATTGATTTGGAGAGTGGCAAGATTACCAATTTCATCAAGTTTGATACTGTAACCTATGTATGGTGACTGGAGGTGCTAA
CTTGGGAAGATTTGGTGTCATCACCAAAAGCGAGAGAGACATCTGGCTCTTTTGTCGTGGTTTATGTAAAAGATGCTAAT
GGCAACAGCTTTGCCACTGGCTCTCCAAAATTTTTGTTATTGGCAAAGGCAATGAACCATGGATTTCTCTTCCCCCAGGA
AAAGGGGTCCACCTCACCATTGCTGAAGAGAGAGGCAAGAAACTGGCAGCCAAACAGAGCAGTGGG

ORF - retro_itri_368 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.44 %
Parental protein coverage: 99.62 %
Number of stop codons detected: 1
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFIK
A.GPKKHLK.VAA.KH....KL....AP.PSTGPHKLRECLPL.IFLRNRL.YALTGDEVK.ICMQ.FIK
RetrocopyAHGPKKHLKWVAALKHGRMGKLDSISAPCPSTGPHKLRECLPLTIFLRNRLNYALTGDEVKNICMQHFIK
ParentalIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPH-LV
IDGKV.TDITYP.GFM.VISI...GENF.LI.DTKG.F.VH.ITPEEAK.KL..VRKIFVGTKGIPH..V
RetrocopyIDGKV*TDITYPTGFMNVISIHTAGENFHLICDTKGHFSVHCITPEEAKSKLGNVRKIFVGTKGIPH>TV
ParentalTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDT-GNLCMVTGGANLGRIGVITNRERH-PGSFDVV
TH....I.YPDPL.K.NDTIQIDLE.GKIT.FIKFDT..NLCMVTGGANLGR.GVIT..ER...GSF.VV
RetrocopyTHNSQMICYPDPLVKMNDTIQIDLESGKITNFIKFDT<CNLCMVTGGANLGRFGVITKSERD>SGSFVVV
ParentalHVKDANGNSFATR-LSNIFVIGKGNKPWISLPRGKGIRLTIAEERDKRLAAKQSSG
.VKDANGNSFAT..LS.IFVIGKGN.PWISLP.GKG..LTIAEER.K.LAAKQSSG
RetrocopyYVKDANGNSFATG<LSKIFVIGKGNEPWISLPPGKGVHLTIAEERGKKLAAKQSSG

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






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_368 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_368 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus 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 23 parental genes, and 150 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146011 retrocopy
retro_acar_82,
Ailuropoda melanoleuca ENSAMEG0000000580514 retrocopies
retro_amel_1003, retro_amel_1128, retro_amel_1296, retro_amel_1381, retro_amel_1695, retro_amel_1869, retro_amel_195, retro_amel_259, retro_amel_327, retro_amel_576, retro_amel_767, retro_amel_869, retro_amel_968, retro_amel_971,
Bos taurus ENSBTAG000000188005 retrocopies
retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris ENSCAFG000000171512 retrocopies
retro_cfam_165, retro_cfam_194,
Callithrix jacchus ENSCJAG000000041922 retrocopies
retro_cjac_19, retro_cjac_361,
Cavia porcellus ENSCPOG000000063373 retrocopies
retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus ENSECAG000000108526 retrocopies
retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Felis catus ENSFCAG0000001204111 retrocopies
retro_fcat_1155, retro_fcat_1498, retro_fcat_1562, retro_fcat_1751, retro_fcat_1773, retro_fcat_2024, retro_fcat_229, retro_fcat_290, retro_fcat_454, retro_fcat_563, retro_fcat_766,
Homo sapiens ENSG000001298241 retrocopy
retro_hsap_1704,
Gorilla gorilla ENSGGOG0000002307918 retrocopies
retro_ggor_1278, retro_ggor_1319, retro_ggor_1354, retro_ggor_1367, retro_ggor_1478, retro_ggor_1479, retro_ggor_1517, retro_ggor_1520, retro_ggor_1689, retro_ggor_223, retro_ggor_2676, retro_ggor_2719, retro_ggor_572, retro_ggor_711, retro_ggor_844, retro_ggor_894, retro_ggor_895, retro_ggor_939,
Loxodonta africana ENSLAFG000000026544 retrocopies
retro_lafr_1007, retro_lafr_1081, retro_lafr_1238, retro_lafr_208,
Meleagris gallopavo ENSMGAG000000096711 retrocopy
retro_mgal_3,
Myotis lucifugus ENSMLUG000000116855 retrocopies
retro_mluc_1638, retro_mluc_2253, retro_mluc_301, retro_mluc_536, retro_mluc_736,
Macaca mulatta ENSMMUG000000032957 retrocopies
retro_mmul_1243, retro_mmul_1589, retro_mmul_1895, retro_mmul_1999, retro_mmul_2338, retro_mmul_43, retro_mmul_97,
Monodelphis domestica ENSMODG000000110701 retrocopy
retro_mdom_238,
Mustela putorius furoENSMPUG0000000529411 retrocopies
retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Mus musculus ENSMUSG0000003132013 retrocopies
retro_mmus_1092, retro_mmus_1686, retro_mmus_2052, retro_mmus_2197, retro_mmus_2487, retro_mmus_2541, retro_mmus_2916, retro_mmus_3025, retro_mmus_3702, retro_mmus_499, retro_mmus_797, retro_mmus_92, retro_mmus_987,
Otolemur garnettii ENSOGAG000000118082 retrocopies
retro_ogar_121, retro_ogar_229,
Pongo abelii ENSPPYG0000002046224 retrocopies
retro_pabe_1005, retro_pabe_1401, retro_pabe_1472, retro_pabe_1524, retro_pabe_1586, retro_pabe_1657, retro_pabe_1673, retro_pabe_1702, retro_pabe_1784, retro_pabe_1948, retro_pabe_2455, retro_pabe_2629, retro_pabe_2836, retro_pabe_2923, retro_pabe_3275, retro_pabe_3325, retro_pabe_340, retro_pabe_493, retro_pabe_579, retro_pabe_580, retro_pabe_679, retro_pabe_891, retro_pabe_921, retro_pabe_954,
Pan troglodytes ENSPTRG000000220259 retrocopies
retro_ptro_1280, retro_ptro_131, retro_ptro_1366, retro_ptro_1367, retro_ptro_1408, retro_ptro_2276, retro_ptro_3032, retro_ptro_728, retro_ptro_784,
Pan troglodytes ENSPTRG000000224701 retrocopy
retro_ptro_1153,
Rattus norvegicus ENSRNOG000000032011 retrocopy
retro_rnor_135,
Ictidomys tridecemlineatus ENSSTOG00000028692 8 retrocopies
retro_itri_1179, retro_itri_1607, retro_itri_291, retro_itri_306, retro_itri_368 , retro_itri_495, retro_itri_738, retro_itri_985,


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