RetrogeneDB ID:

retro_mmus_92

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:6:148354709..148355498(+)
Located in intron of:ENSMUSG00000030306
Retrocopy
information
Ensembl ID:ENSMUSG00000063171
Aliases:Rps4l, 1110033J19Rik, AA407494, Rps4y2
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Rps4x
Ensembl ID:ENSMUSG00000031320
Aliases:Rps4x, Rps4, Rps4-1
Description:ribosomal protein S4, X-linked [Source:MGI Symbol;Acc:MGI:98158]


Retrocopy-Parental alignment summary:






>retro_mmus_92
ATGGCTCGTGGTCCCAAGAAACACCTGAAGCGTGTGGCGGCCCCACGCCACTGGATGCTGGACAAACTGACCGGTGTGTT
CGCGCCCCGTCCGTCTGCCGGCCCGCACCGCCTGCGGGAGTGCCTGCCGCTCGCCATCTTCCTGAGGAACAGGCTCAAGT
ACGCCCTGACCGGCGACGAGGTGAAGAAGATCTGCATGCAGCGGCTCATTAAGGTCGACGGCAAGGTCAGAACCGATGTG
GCCTACCCAGCTGGCTTCATGGATGTCATCAGCATCGACAAGAGCGGCGAGAACTTCCGCCTCGTCTACGACACCAAGGG
CCGCTTCGCGGTACACCGCATCACGCCCGAGGAGGCCAAGTACAAGCTGTGCAAGGTGAGGAAAGTCTTCGTGGGTACCA
AGGGCATCCCGCACCTCGTCACGCACGACGCGCGTACCATCCGCTACCCTGACCCGCTCATCAAGGTCAACGACACCGTG
CAGATCTCGCTAGACAGCGGAAAAATCACCGATGCCATCAAGTTTGATACCGGCAACCTGTGCATGGTAACCGGAGGCGC
CAACCTGGGTCGCATCGGCGTCATCACCAACCGCGAGCGCCACCCCGGCTCCTTTGACGTGGTCCACGTGAAAGATGCCA
ACGGCAATGGCTTCGCTACCCGCCTCTCCAACATCTTCGTGATCGGGAAGGGCAACAAGCCGTGGATCTCCCTTCCCCGG
GGAAAAGGAATCCGCCTCACCATTGCCGAAGAGAGAGACAAGAGGCTGGCGGCCAAGCAGAGCGGGTGA

ORF - retro_mmus_92 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.49 %
Parental protein coverage: 99.24 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFI
MARGPKKHLKRVAAP.HWMLDKLTGVFAPRPS.GPH.LRECLPL.IFLRNRLKYALTGDEVKKICMQR.I
RetrocopyMARGPKKHLKRVAAPRHWMLDKLTGVFAPRPSAGPHRLRECLPLAIFLRNRLKYALTGDEVKKICMQRLI
ParentalKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHLV
K.DGKVRTD..YPAGFMDVISIDK.GENFRL.YDTKGRFAVHRITPEEAKYKLCKVRK.FVGTKGIPHLV
RetrocopyKVDGKVRTDVAYPAGFMDVISIDKSGENFRLVYDTKGRFAVHRITPEEAKYKLCKVRKVFVGTKGIPHLV
ParentalTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVHV
THDARTIRYPDPLIKVNDT.QI.L..GKITD.IKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVHV
RetrocopyTHDARTIRYPDPLIKVNDTVQISLDSGKITDAIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVHV
ParentalKDANGNSFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEERDKRLAAKQS
KDANGN.FATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEERDKRLAAKQS
RetrocopyKDANGNGFATRLSNIFVIGKGNKPWISLPRGKGIRLTIAEERDKRLAAKQS

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
SRP007412_brain 8 .36 RPM 93 .43 RPM
SRP007412_cerebellum 9 .42 RPM 46 .29 RPM
SRP007412_heart 10 .12 RPM 123 .84 RPM
SRP007412_kidney 8 .01 RPM 110 .38 RPM
SRP007412_liver 8 .93 RPM 108 .09 RPM
SRP007412_testis 47 .61 RPM 8 .42 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_92 was not detected

EST - click to see more details

45 EST(s) were mapped to retro_mmus_92 retrocopy
EST ID Start End Identity Match Mis-match Score
AA500014 148355006 148355264 100 255 0 253
AI325738 148354727 148355098 96.3 360 11 348
AL117823 148354671 148354928 97.3 257 0 254
AV451715 148354668 148355098 99.8 429 0 427
AV462502 148354676 148355103 100 426 0 425
AV463810 148354666 148355103 100 436 0 435
AV464024 148354682 148355097 99.6 410 1 404
AV465962 148354666 148354985 100 316 0 314
AV466506 148354705 148355142 100 437 0 437
AV472090 148354708 148355009 99 294 3 289
AV472928 148354700 148355113 100 413 0 413
AV472933 148354673 148355069 99.8 390 1 385
AV482075 148354677 148355090 99.8 410 0 406
AV483695 148354676 148355097 100 419 0 417
AV493432 148354697 148355087 99.8 389 1 388
AV494405 148354764 148354985 100 221 0 221
AV496116 148354671 148355008 100 337 0 337
AV498101 148354661 148355099 99.8 436 1 434
AV500341 148354778 148355152 100 374 0 374
AV503345 148354681 148355096 98.8 415 0 413
AV506464 148354672 148355100 100 426 0 425
AV506996 148354671 148355099 99.8 425 1 422
AV510526 148354666 148355092 99.8 421 1 416
AV511272 148354666 148355095 99.8 426 0 422
AV511384 148354669 148355107 99.8 435 1 432
AV515777 148354666 148355103 100 436 0 435
AV516234 148354683 148355068 99.8 380 0 376
AV575050 148354720 148355029 98.8 307 1 304
AV581407 148354695 148355058 98.7 361 2 358
AV581989 148354677 148354982 100 305 0 305
AV586344 148354708 148355136 98.4 420 7 412
BF012952 148354734 148355078 99.5 342 2 340
BU605011 148354789 148354979 99 188 2 186
BY029273 148354664 148355097 100 381 0 380
BY034424 148354709 148355085 99.5 373 2 371
BY036867 148354657 148355029 99.8 368 1 367
BY096065 148354679 148355071 100 391 0 391
BY114163 148354657 148354973 100 316 0 316
BY115419 148354657 148354996 99.8 338 1 337
BY321323 148354709 148355056 100 346 0 346
BY328788 148354657 148354990 99.4 331 2 329
CJ163072 148354657 148355047 100 390 0 390
CJ164673 148354657 148355078 100 421 0 421
CJ171908 148354686 148355065 100 379 0 379
D76864 148354671 148354962 96.9 285 2 274

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_120399131 libraries 16 libraries 223 libraries 102 libraries 600 libraries
TSS #2 TSS_120400224 libraries 141 libraries 218 libraries 205 libraries 284 libraries
TSS #3 TSS_120401777 libraries 237 libraries 48 libraries 10 libraries 0 libraries
TSS #4 TSS_120402864 libraries 167 libraries 40 libraries 1 library 0 libraries

The graphical summary, for retro_mmus_92 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_92 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_92 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 26 parental genes, and 246 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146011 retrocopy
retro_acar_82,
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,
Homo sapiens ENSG000001298241 retrocopy
retro_hsap_1704,
Homo sapiens ENSG0000019803419 retrocopies
retro_hsap_1070, retro_hsap_1151, retro_hsap_120, retro_hsap_1204, retro_hsap_1792, retro_hsap_1868, retro_hsap_2026, retro_hsap_2051, retro_hsap_2052, retro_hsap_2270, retro_hsap_2437, retro_hsap_2443, retro_hsap_3162, retro_hsap_3423, retro_hsap_3519, retro_hsap_3986, retro_hsap_4051, retro_hsap_656, retro_hsap_875,
Loxodonta africana ENSLAFG000000026544 retrocopies
retro_lafr_1007, retro_lafr_1081, retro_lafr_1238, retro_lafr_208,
Macropus eugenii ENSMEUG0000000796916 retrocopies
retro_meug_131, retro_meug_141, retro_meug_1644, retro_meug_1732, retro_meug_1814, retro_meug_194, retro_meug_2098, retro_meug_2121, retro_meug_228, retro_meug_562, retro_meug_628, retro_meug_673, retro_meug_843, retro_meug_872, retro_meug_972, retro_meug_999,
Meleagris gallopavo ENSMGAG000000096711 retrocopy
retro_mgal_3,
Microcebus murinus ENSMICG0000001660658 retrocopies
retro_mmur_1107, retro_mmur_1108, retro_mmur_1123, retro_mmur_1136, retro_mmur_1168, retro_mmur_1208, retro_mmur_1209, retro_mmur_1229, retro_mmur_1231, retro_mmur_1257, retro_mmur_1268, retro_mmur_1334, retro_mmur_1411, retro_mmur_1416, retro_mmur_1430, retro_mmur_1442, retro_mmur_1454, retro_mmur_1467, retro_mmur_1471, retro_mmur_1519, retro_mmur_1578, retro_mmur_1584, retro_mmur_1599, retro_mmur_1600, retro_mmur_1611, retro_mmur_166, retro_mmur_241, retro_mmur_281, retro_mmur_289, retro_mmur_293, retro_mmur_347, retro_mmur_363, retro_mmur_390, retro_mmur_510, retro_mmur_511, retro_mmur_521, retro_mmur_523, retro_mmur_530, retro_mmur_54, retro_mmur_551, retro_mmur_591, retro_mmur_609, retro_mmur_619, retro_mmur_663, retro_mmur_665, retro_mmur_687, retro_mmur_767, retro_mmur_784, retro_mmur_828, retro_mmur_840, retro_mmur_917, retro_mmur_918, retro_mmur_931, retro_mmur_943, retro_mmur_946, retro_mmur_949, retro_mmur_96, retro_mmur_995,
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 ENSMUSG00000031320 13 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,
Nomascus leucogenys ENSNLEG0000001812125 retrocopies
retro_nleu_1127, retro_nleu_1226, retro_nleu_1361, retro_nleu_142, retro_nleu_1442, retro_nleu_1907, retro_nleu_1908, retro_nleu_2089, retro_nleu_2256, retro_nleu_244, retro_nleu_2461, retro_nleu_2495, retro_nleu_2587, retro_nleu_2613, retro_nleu_2640, retro_nleu_2646, retro_nleu_2776, retro_nleu_2801, retro_nleu_2932, retro_nleu_2967, retro_nleu_2968, retro_nleu_486, retro_nleu_500, retro_nleu_560, retro_nleu_947,
Otolemur garnettii ENSOGAG000000118082 retrocopies
retro_ogar_121, retro_ogar_229,
Procavia capensis ENSPCAG000000007613 retrocopies
retro_pcap_334, retro_pcap_35, retro_pcap_360,
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,
Pteropus vampyrus ENSPVAG0000001288221 retrocopies
retro_pvam_1021, retro_pvam_1082, retro_pvam_1158, retro_pvam_1264, retro_pvam_1298, retro_pvam_1312, retro_pvam_1327, retro_pvam_1364, retro_pvam_1419, retro_pvam_177, retro_pvam_191, retro_pvam_214, retro_pvam_219, retro_pvam_335, retro_pvam_473, retro_pvam_628, retro_pvam_714, retro_pvam_809, retro_pvam_835, retro_pvam_921, retro_pvam_930,
Rattus norvegicus ENSRNOG000000032011 retrocopy
retro_rnor_135,
Sus scrofa ENSSSCG000000124055 retrocopies
retro_sscr_1070, retro_sscr_563, retro_sscr_580, retro_sscr_665, retro_sscr_973,
Ictidomys tridecemlineatus ENSSTOG000000286928 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,
Vicugna pacos ENSVPAG000000109524 retrocopies
retro_vpac_244, retro_vpac_460, retro_vpac_604, retro_vpac_653,


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