RetrogeneDB ID:

retro_rnor_239

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:3:8751718..8752492(+)
Located in intron of:ENSRNOG00000017883
Retrocopy
information
Ensembl ID:ENSRNOG00000032635
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL8
Ensembl ID:ENSRNOG00000048523
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_rnor_239
ATGGGCCGTGTGATCCGAGGCCAGAGGAAAGGTGCCGGTTCTGTGTTTCGTGCGCACGTGAAGCACCGTAAGGGAGCCGC
GCGTCTGCGTGCTGTGGACTTCGCGGAGCGACACGGCTACATTAAAGGCATCGTAAAGGACATCATTCATGACCCTGGCC
GCGGCGCTCCCCTCGCGAAAGTAGTCTTTCGTGATCCCTATCGATTCAAGAAGCGGACAGAGCTGTTCATCGCCGCAGAG
GGAATCCACACTGGACAGTTTGTGTACTGCGGCAAGAAGGCCCAGCTGAATATTGGCAATGTTTTGCCCGTGGGCACCAT
GCCTGAGGGTACTATCGTGTGTTGTCTGGAGGAGAAGCCTGGGGACAGGGGCAAGCTGGCACGAGCCTCCGGGAACTATG
CTACAGTCATCTCCCACAACCCAGAGACCAAGAAGACCCGAGTGAAGCTGCCTTCAGGGTCCAAGAAGGTCATTTCCTCT
GCTAACCGAGCTGTTGTTGGTGTCGTGGCTGGCGGGGGCAGAATTGACAAGCCTATCTTAAAGGCTGGCCGTGCCTACCA
TAAGTACAAGGCAAAGAGGAACTGCTGGCCACGTGTGCGGGGTGTTGCCATGAATCCTGTGGAGCATCCCTTTGGCGGTG
GTAACCACCAGCACATTGGCAAGCCTTCCACTATCCGAAGAGATGCCCCAGCTGGGCGCAAAGTGGGTCTCATTGCTGCC
CGCCGGACTGGACGGCTACGTGGAACCAAAACTGTACAGGAGAAGGAGAACTAG

ORF - retro_rnor_239 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 100. %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKVVFRDPYRFK
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKVVFRDPYRFK
RetrocopyMGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKVVFRDPYRFK
ParentalKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHN
KRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHN
RetrocopyKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHN
ParentalPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRGVAMNPVEHP
PETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRGVAMNPVEHP
RetrocopyPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRGVAMNPVEHP
ParentalFGGGNHQHIGKPSTIRRDAPAGRKVGLIAARRTGRLRGTKTVQEKEN
FGGGNHQHIGKPSTIRRDAPAGRKVGLIAARRTGRLRGTKTVQEKEN
RetrocopyFGGGNHQHIGKPSTIRRDAPAGRKVGLIAARRTGRLRGTKTVQEKEN

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
SRP017611_brain 6 .97 RPM 0 .00 RPM
SRP017611_kidney 7 .33 RPM 0 .00 RPM
SRP017611_liver 4 .77 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

43 EST(s) were mapped to retro_rnor_239 retrocopy
EST ID Start End Identity Match Mis-match Score
AA684845 8751930 8752201 100 266 0 266
AA685320 8751730 8752032 99.4 294 1 291
AA685482 8751693 8752012 99.4 312 0 309
AA685549 8751702 8751998 99.7 289 0 287
AA685689 8751723 8751950 98.7 217 1 212
AA685768 8751793 8752165 99.2 365 2 361
AA686646 8751711 8751963 99.6 247 0 245
AA687046 8751703 8751942 98.3 229 3 224
BE127801 8751703 8752071 100 367 0 366
BE128597 8751699 8752071 100 372 0 372
BP493232 8751706 8752055 100 349 0 349
CB706266 8751696 8752085 100 389 0 389
CB795308 8751696 8752112 100 416 0 416
DW287865 8752045 8752285 100 240 0 240
DW294300 8752045 8752285 100 235 0 235
DW298237 8752045 8752273 100 227 0 227
DW300685 8752045 8752286 99.2 230 2 228
DW304813 8752045 8752285 100 238 0 238
DW307469 8752045 8752285 100 238 0 238
DW312084 8752046 8752285 98.3 223 4 219
DW312598 8752045 8752285 100 240 0 240
DW316498 8752045 8752269 99.6 218 1 217
DW317757 8752045 8752224 98.3 165 3 162
DW326190 8752045 8752285 100 239 0 239
DW328006 8752046 8752285 99.6 238 1 237
DW329270 8752045 8752285 99.2 231 2 229
DW330782 8752045 8752285 99.6 230 1 229
DW334257 8752045 8752286 99.2 230 2 228
DW380802 8751829 8751985 100 156 0 156
DW382085 8752045 8752285 99.6 239 1 238
DW382234 8752045 8752285 99.2 238 2 236
DW383028 8752045 8752284 99.2 237 2 235
DW383392 8752045 8752285 99.6 238 1 236
DW383393 8752045 8752285 99.6 239 1 238
DW385731 8752045 8752285 98.4 236 4 232
DW387851 8752045 8752285 100 240 0 240
DW389175 8752045 8752285 99.6 239 1 238
DW389178 8752045 8752285 98 235 5 230
DW392198 8752045 8752285 100 240 0 240
DW393613 8752045 8752285 99.2 238 2 236
FM051657 8751711 8752026 99.7 313 1 312
FN806676 8751692 8752065 100 373 0 373
H34970 8751705 8752093 99 377 3 372

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_239 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_239 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000179331 retrocopy
retro_acar_31,
Ailuropoda melanoleuca ENSAMEG000000053951 retrocopy
retro_amel_241,
Bos taurus ENSBTAG000000263271 retrocopy
retro_btau_96,
Canis familiaris ENSCAFG000000016771 retrocopy
retro_cfam_1132,
Callithrix jacchus ENSCJAG000000213884 retrocopies
retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Cavia porcellus ENSCPOG000000038542 retrocopies
retro_cpor_1006, retro_cpor_1415,
Dasypus novemcinctus ENSDNOG000000093002 retrocopies
retro_dnov_2505, retro_dnov_503,
Echinops telfairi ENSETEG000000071044 retrocopies
retro_etel_1100, retro_etel_264, retro_etel_296, retro_etel_916,
Felis catus ENSFCAG000000262881 retrocopy
retro_fcat_570,
Homo sapiens ENSG000001610161 retrocopy
retro_hsap_2851,
Gorilla gorilla ENSGGOG000000081641 retrocopy
retro_ggor_1974,
Macropus eugenii ENSMEUG000000138249 retrocopies
retro_meug_1116, retro_meug_1354, retro_meug_1757, retro_meug_1817, retro_meug_1881, retro_meug_670, retro_meug_941, retro_meug_960, retro_meug_974,
Macaca mulatta ENSMMUG000000133792 retrocopies
retro_mmul_1470, retro_mmul_1531,
Monodelphis domestica ENSMODG000000042833 retrocopies
retro_mdom_1055, retro_mdom_1696, retro_mdom_253,
Mustela putorius furoENSMPUG000000060221 retrocopy
retro_mputfur_1517,
Mus musculus ENSMUSG000000039702 retrocopies
retro_mmus_2004, retro_mmus_2112,
Nomascus leucogenys ENSNLEG000000109522 retrocopies
retro_nleu_1603, retro_nleu_594,
Ornithorhynchus anatinus ENSOANG000000026461 retrocopy
retro_oana_93,
Oryctolagus cuniculus ENSOCUG000000247161 retrocopy
retro_ocun_146,
Pan troglodytes ENSPTRG000000207161 retrocopy
retro_ptro_1931,
Rattus norvegicus ENSRNOG00000048523 2 retrocopies
retro_rnor_122, retro_rnor_239 ,
Sarcophilus harrisii ENSSHAG000000135682 retrocopies
retro_shar_482, retro_shar_558,
Tupaia belangeri ENSTBEG000000103632 retrocopies
retro_tbel_2826, retro_tbel_3453,
Tursiops truncatus ENSTTRG000000138581 retrocopy
retro_ttru_1147,




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