RetrogeneDB ID:

retro_rnor_113

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:10:112140975..112141869(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000037220
Aliases:Rpl5l1, RGD1564051
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Rpl5
Ensembl ID:ENSRNOG00000023529
Aliases:None
Description:60S ribosomal protein L5 [Source:UniProtKB/Swiss-Prot;Acc:P09895]


Retrocopy-Parental alignment summary:






>retro_rnor_113
ATGGGGTTCATGAAAGTTGTCAAGAATAAGGCCTACTTTAAAAGATACCAAGTGAGATTTAGAAGGTGGCGAGGGGGTAA
AACTGACTACTGTGCACGGAAACGATTGGTGGTCCAGGACAAAAATAAGTACAACACACCAAAATACAGGATGATAGTTC
GTGTAACGAACAGAGACATCATCTGCCAGATTGCATATGCCCGTATAGAAGGGGATATGATCGTCTGTGCACCATATGCA
CATGAACTTCCAAAATACGGTGTGAAAGTTGGCTTGACAAACTATGCTGCAGCCTATTGCACTGGCCTGCTGCTGGCCCG
CAGGCTTCTGAATAGGTTTGGCATGGACAAGATCTATGAAGGCCAAGTGGAGGTGAATGGAGACGAGTACAATGTGGAAA
GCATTGACGGTCAGCCTGGTGCCTTCACTTGCTATTTGGATGCGGGTCTTGCCCGAACTACAACTGGCAATAAAGTTTTT
GGCGCCCTGAAGGGAGCTGTGGATGGAGTCTTGTCTATCCCCCATAGTACCAAACGATTCCCTGGCCATGACTCTGAAAG
CAAGGAGTTCAATGCAGAGGTGCACCGGAAGCACATCATGGGTCAGAATGTGGCAGACTACATGCGCTACCTGATGGAGG
AGGATGAGGATGCGTATAAGAAACAGTTCTCTCAGTACATCAAGAACAACGTGACTCCAGACATGATGGAGGAGATGTAT
AAGAAAGCTCATGCTGCTATCCGAGAGAATCCAGTCTATGACAAGAAGCCCAAGAGAGAAGTGAAGAAGAAGAGGTGGAA
TCGTCCCAAAATGTCTCTTGCCCAGAAGAAAGACCGGGTTGCTCAAAAGAAGGCAAGCTTCCTCAGAGCTCAGGAATGGG
CTGCTGAAAGCTAA

ORF - retro_rnor_113 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.63 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMGFVKVVKNKAYFKRYQVRFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIE
MGF.KVVKNKAYFKRYQVRFRR.R.GKTDY.ARKRLV.QDKNKYNTPKYRMIVRVTNRDIICQIAYARIE
RetrocopyMGFMKVVKNKAYFKRYQVRFRRWRGGKTDYCARKRLVVQDKNKYNTPKYRMIVRVTNRDIICQIAYARIE
ParentalGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVNGDEYNVESIDGQPG
GDMIVCA.YAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVNGDEYNVESIDGQPG
RetrocopyGDMIVCAPYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVNGDEYNVESIDGQPG
ParentalAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRY
AFTCYLDAGLARTTTGNKVFGALKGAVDG.LSIPHSTKRFPG.DSESKEFNAEVHRKHIMGQNVADYMRY
RetrocopyAFTCYLDAGLARTTTGNKVFGALKGAVDGVLSIPHSTKRFPGHDSESKEFNAEVHRKHIMGQNVADYMRY
ParentalLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRV
LMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVY.KKPKREVKKKRWNRPKMSLAQKKDRV
RetrocopyLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVYDKKPKREVKKKRWNRPKMSLAQKKDRV
ParentalAQKKASFLRAQERAAES
AQKKASFLRAQE.AAES
RetrocopyAQKKASFLRAQEWAAES

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 1 .65 RPM 103 .75 RPM
SRP017611_kidney 2 .72 RPM 183 .25 RPM
SRP017611_liver 2 .02 RPM 112 .29 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_113 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_113 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_113 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 66 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098785 retrocopies
retro_amel_1200, retro_amel_137, retro_amel_139, retro_amel_1439, retro_amel_1669,
Bos taurus ENSBTAG000000020262 retrocopies
retro_btau_120, retro_btau_67,
Cavia porcellus ENSCPOG000000006988 retrocopies
retro_cpor_1047, retro_cpor_1097, retro_cpor_1141, retro_cpor_1259, retro_cpor_1354, retro_cpor_1387, retro_cpor_428, retro_cpor_737,
Dipodomys ordii ENSDORG000000056742 retrocopies
retro_dord_226, retro_dord_670,
Equus caballus ENSECAG000000210651 retrocopy
retro_ecab_654,
Macropus eugenii ENSMEUG000000063613 retrocopies
retro_meug_1168, retro_meug_1537, retro_meug_2146,
Monodelphis domestica ENSMODG000000116351 retrocopy
retro_mdom_748,
Mustela putorius furoENSMPUG000000041506 retrocopies
retro_mputfur_213, retro_mputfur_449, retro_mputfur_451, retro_mputfur_597, retro_mputfur_721, retro_mputfur_833,
Mus musculus ENSMUSG0000005855811 retrocopies
retro_mmus_1000, retro_mmus_1185, retro_mmus_1338, retro_mmus_1789, retro_mmus_1991, retro_mmus_2577, retro_mmus_2846, retro_mmus_297, retro_mmus_3076, retro_mmus_504, retro_mmus_911,
Ornithorhynchus anatinus ENSOANG000000046691 retrocopy
retro_oana_97,
Oryctolagus cuniculus ENSOCUG000000100892 retrocopies
retro_ocun_265, retro_ocun_54,
Petromyzon marinus ENSPMAG000000020401 retrocopy
retro_pmar_23,
Pteropus vampyrus ENSPVAG000000151174 retrocopies
retro_pvam_1427, retro_pvam_355, retro_pvam_505, retro_pvam_527,
Rattus norvegicus ENSRNOG00000023529 6 retrocopies
retro_rnor_113 , retro_rnor_2246, retro_rnor_2418, retro_rnor_2498, retro_rnor_2802, retro_rnor_2922,
Sarcophilus harrisii ENSSHAG000000064171 retrocopy
retro_shar_202,
Sus scrofa ENSSSCG000000068992 retrocopies
retro_sscr_149, retro_sscr_219,
Tupaia belangeri ENSTBEG000000105605 retrocopies
retro_tbel_101, retro_tbel_1054, retro_tbel_1518, retro_tbel_3006, retro_tbel_3530,
Tursiops truncatus ENSTTRG000000130975 retrocopies
retro_ttru_1446, retro_ttru_1548, retro_ttru_1796, retro_ttru_645, retro_ttru_979,


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