RetrogeneDB ID:

retro_itri_1106

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393376.1:3669610..3670189(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL9
Ensembl ID:ENSSTOG00000002077
Aliases:None
Description:ribosomal protein L9 [Source:HGNC Symbol;Acc:10369]


Retrocopy-Parental alignment summary:






>retro_itri_1106
ATGAAGACACTTCTCAGCAATGAGACTGTCGACATTTCAGAAAATGTCAACAGCACTCTGAAGGGAAGCACAGTTCTTGT
GAAGGGCCCAAGAGGAACCCTCTGGAGGGATTTCAATCATATCAATGTAGAACTCAGTTTCCTTGGAAAGAAAAAGAAGA
GGCTACGAGTTGACAAGTGGTGGGGAAATAGAAAGGAACTGGCCACTGTCCACACCATGTGCAGTCATTTAGAGAACATG
ACCAAGGGTGTTACACTGGGCTTCCATTACAAGGTGAGATCTGTGTCTGCTTACTTCCCCATCAACGTTTTTATTCAGGA
GAATGAGTCTCTTCTTGAAATCTGAAATTTCTTGGATGAAAAATATATCTGCAGGATTCGGATGAAGACAGGTATTGCTT
GTTCAGTGTCTCAAACTCAGAAAGACAAATTAATCTTTGAAGGAAATGATATTGAACTTGTTATGAATTCAGCAGCTTTA
ATTCAGCAAGCCACAACAGTGAAAAAAAAGAAGGATATCAGAAAAATTTTGGATGATATGTATGTTTCTGAAAAAGAAAC
AGTTCAGCAGGCTGATGAA

ORF - retro_itri_1106 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.31 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMKTILSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKWWGNRKELATV
MKT.LSN.TVDI.ENV..TLKG.TV.VKGPRGTL.RDFNHINVELS.LGKKKKRLRVDKWWGNRKELATV
RetrocopyMKTLLSNETVDISENVNSTLKGSTVLVKGPRGTLWRDFNHINVELSFLGKKKKRLRVDKWWGNRKELATV
ParentalRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGEKYIRRVRMRTGVACSVSQAQ
.T.CSH..NM.KGVTLGF.YK.RSV.A.FPINV.IQEN.SL.EI.NFL.EKYI.R.RM.TG.ACSVSQ.Q
RetrocopyHTMCSHLENMTKGVTLGFHYKVRSVSAYFPINVFIQENESLLEI*NFLDEKYICRIRMKTGIACSVSQTQ
ParentalKDELILEGNDIELVSNSAALIQQATTV-KNKDIRKFLDGIYVSEKGTVQQADE
KD.LI.EGNDIELV.NSAALIQQATTV...KDIRK.LD..YVSEK.TVQQADE
RetrocopyKDKLIFEGNDIELVMNSAALIQQATTVXXXKDIRKILDDMYVSEKETVQQADE

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_1106 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1106 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 15 parental genes, and 176 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000073171 retrocopy
retro_acar_163,
Cavia porcellus ENSCPOG0000000454315 retrocopies
retro_cpor_1037, retro_cpor_1160, retro_cpor_1264, retro_cpor_1400, retro_cpor_1483, retro_cpor_182, retro_cpor_346, retro_cpor_354, retro_cpor_395, retro_cpor_472, retro_cpor_530, retro_cpor_565, retro_cpor_628, retro_cpor_665, retro_cpor_684,
Danio rerio ENSDARG000000373501 retrocopy
retro_drer_18,
Dasypus novemcinctus ENSDNOG0000000741118 retrocopies
retro_dnov_1298, retro_dnov_1560, retro_dnov_1684, retro_dnov_1845, retro_dnov_1877, retro_dnov_1936, retro_dnov_2148, retro_dnov_2277, retro_dnov_2624, retro_dnov_2659, retro_dnov_282, retro_dnov_407, retro_dnov_437, retro_dnov_450, retro_dnov_615, retro_dnov_787, retro_dnov_82, retro_dnov_975,
Dipodomys ordii ENSDORG000000010886 retrocopies
retro_dord_276, retro_dord_42, retro_dord_435, retro_dord_604, retro_dord_637, retro_dord_718,
Erinaceus europaeus ENSEEUG0000000439439 retrocopies
retro_eeur_11, retro_eeur_136, retro_eeur_153, retro_eeur_162, retro_eeur_184, retro_eeur_191, retro_eeur_229, retro_eeur_246, retro_eeur_27, retro_eeur_279, retro_eeur_280, retro_eeur_282, retro_eeur_296, retro_eeur_307, retro_eeur_352, retro_eeur_383, retro_eeur_399, retro_eeur_410, retro_eeur_429, retro_eeur_433, retro_eeur_449, retro_eeur_453, retro_eeur_461, retro_eeur_471, retro_eeur_486, retro_eeur_493, retro_eeur_51, retro_eeur_540, retro_eeur_572, retro_eeur_590, retro_eeur_599, retro_eeur_600, retro_eeur_619, retro_eeur_624, retro_eeur_65, retro_eeur_670, retro_eeur_678, retro_eeur_68, retro_eeur_98,
Gadus morhua ENSGMOG000000010021 retrocopy
retro_gmor_28,
Macropus eugenii ENSMEUG000000167228 retrocopies
retro_meug_1087, retro_meug_1411, retro_meug_1961, retro_meug_22, retro_meug_440, retro_meug_490, retro_meug_650, retro_meug_763,
Myotis lucifugus ENSMLUG0000000459734 retrocopies
retro_mluc_1028, retro_mluc_1029, retro_mluc_1261, retro_mluc_1269, retro_mluc_127, retro_mluc_1320, retro_mluc_1368, retro_mluc_1380, retro_mluc_1572, retro_mluc_1655, retro_mluc_1704, retro_mluc_1757, retro_mluc_1813, retro_mluc_1858, retro_mluc_1880, retro_mluc_1983, retro_mluc_2041, retro_mluc_2067, retro_mluc_2112, retro_mluc_2119, retro_mluc_220, retro_mluc_2229, retro_mluc_223, retro_mluc_2230, retro_mluc_2370, retro_mluc_2428, retro_mluc_2495, retro_mluc_2611, retro_mluc_293, retro_mluc_461, retro_mluc_533, retro_mluc_648, retro_mluc_75, retro_mluc_895,
Monodelphis domestica ENSMODG000000205537 retrocopies
retro_mdom_1026, retro_mdom_1078, retro_mdom_1261, retro_mdom_1352, retro_mdom_1414, retro_mdom_401, retro_mdom_637,
Mus musculus ENSMUSG000000472152 retrocopies
retro_mmus_262, retro_mmus_81,
Otolemur garnettii ENSOGAG0000000493520 retrocopies
retro_ogar_117, retro_ogar_1223, retro_ogar_1471, retro_ogar_1614, retro_ogar_1694, retro_ogar_1807, retro_ogar_1884, retro_ogar_1906, retro_ogar_1933, retro_ogar_2162, retro_ogar_2173, retro_ogar_2806, retro_ogar_3036, retro_ogar_3115, retro_ogar_3276, retro_ogar_329, retro_ogar_429, retro_ogar_864, retro_ogar_886, retro_ogar_963,
Rattus norvegicus ENSRNOG000000267163 retrocopies
retro_rnor_237, retro_rnor_310, retro_rnor_332,
Sarcophilus harrisii ENSSHAG000000049188 retrocopies
retro_shar_191, retro_shar_192, retro_shar_236, retro_shar_340, retro_shar_359, retro_shar_406, retro_shar_600, retro_shar_607,
Ictidomys tridecemlineatus ENSSTOG00000002077 13 retrocopies
retro_itri_1106 , retro_itri_1182, retro_itri_1328, retro_itri_305, retro_itri_313, retro_itri_339, retro_itri_392, retro_itri_588, retro_itri_663, retro_itri_838, retro_itri_908, retro_itri_914, retro_itri_956,


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