RetrogeneDB ID:

retro_mmus_1131

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:13:91261432..91262423(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Hnrnpk
Ensembl ID:ENSMUSG00000021546
Aliases:Hnrnpk, Hnrpk, KBBP, NOVA
Description:heterogeneous nuclear ribonucleoprotein K [Source:MGI Symbol;Acc:MGI:99894]


Retrocopy-Parental alignment summary:






>retro_mmus_1131
CAGTACCAACATTATAAAGGAAGTGACTTTGATTGCGAGTTGAGACTGTTGATTCATCAGAGTCTGGCAGGAGGAATAAT
TGGTGTTAAAGGTGCTAAAATCAAAGAACTTCGAGAAAACACTCAGACAACAATCAAGCTTTTCCAGGAGTGCTGCCCTC
ACTCTACTGACAGAGTTGTTCTTATTGGAGGAAAACCTGATAGGGTTGTAGAATGCATTAAGATCATCCTTCACCTTATA
TCTGAGTCTCCTATCAAAGGACGTGCACAACCGTATGATCCCAACTTTTATGATGAGACCTATGATTATGGTGGTTTTAC
AATGATGTTTGATGACCGCTGAGGATGACCTGTGGGATTCCCCATGAGGGGAAGAGGTGGTTTTGACAGAATGCCTCCTG
GTCAGGGTGGGCGTCCTATGCCTCCTTCTAGAAGAGATTATGATGATATGAGCCCTTGTCGAGGACCTCCACCACCTCCT
CCTGGTCGAGGTGGCCGGGGTGGCAGCAGAGCCCGGAATCCTCTTCTTCCTCCACCACCACCCAGAGGGGGAGATCTAAT
GGCTTATGACAGAAGAGGAAGGCCTGGAGACCGCTATGATGGCATGGTTGGGTTCAGTGCTGATGAAACTTGGGACTCTG
CAATTGACACATGGAGCCCATCAGAATGGCAAATGGCTTATGAACCACAGGGTGGTTCTGGATATGACTATTCTTATGCA
GGGGGGTCGTGGCTCATATGGTGATCTTGGCGGACCTATTATCACTATACAAGTAACTATTCCCAAAGATTTGGCTGGAT
CTATTATTGCCAAAGGTGGTCAGCGGATTAAACAAATTTGTCATGAATCTGGAGCATCAATCAAAATTGATGAACCTTTA
GATGGATCTGAAGATCGGATCATTACCATTACAGGAACACAGGGCCAGATACAGAATACACAGTATTTGCTGCAGAACAG
TGTGAAGCAGTATGCAGATGTTGAAGGATTC

ORF - retro_mmus_1131 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.48 %
Parental protein coverage: 75.23 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalEYQHYKGSDFDCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVV
.YQHYKGSDFDCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVV
RetrocopyQYQHYKGSDFDCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVV
ParentalECIKIILDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPM
ECIKIIL.LISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDR.G.PVGFPMRGRGGFDRMPPG.GGRPM
RetrocopyECIKIILHLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDR*G*PVGFPMRGRGGFDRMPPGQGGRPM
ParentalPPSRRDYDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADE
PPSRRDYDDMSP.RGPPPPPPGRGGRGGSRARN.PL.PPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADE
RetrocopyPPSRRDYDDMSPCRGPPPPPPGRGGRGGSRARN-PLLPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADE
ParentalTWDSAIDTWSPSEWQMAYEPQGGSGYDYSYA-GGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQ
TWDSAIDTWSPSEWQMAYEPQGGSGYDYSYA.GGRGSYGDLGGPIIT.QVTIPKDLAGSII.KGGQRIKQ
RetrocopyTWDSAIDTWSPSEWQMAYEPQGGSGYDYSYA>GGRGSYGDLGGPIITIQVTIPKDLAGSIIAKGGQRIKQ
ParentalIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYADVEGF
I.HESGASIKIDEPL.GSEDRIITITGTQ.QIQN.QYLLQNSVKQYADVEGF
RetrocopyICHESGASIKIDEPLDGSEDRIITITGTQGQIQNTQYLLQNSVKQYADVEGF

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 1 .78 RPM 205 .71 RPM
SRP007412_cerebellum 2 .82 RPM 176 .42 RPM
SRP007412_heart 2 .52 RPM 146 .65 RPM
SRP007412_kidney 3 .16 RPM 198 .58 RPM
SRP007412_liver 2 .62 RPM 172 .59 RPM
SRP007412_testis 2 .97 RPM 166 .26 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1131 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1131 retrocopy.

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_3148399 libraries141 libraries581 libraries147 libraries104 libraries

The graphical summary, for retro_mmus_1131 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_1131 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1131 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000211312 retrocopies
retro_btau_468, retro_btau_605,
Dasypus novemcinctus ENSDNOG000000000264 retrocopies
retro_dnov_1433, retro_dnov_1820, retro_dnov_2316, retro_dnov_2638,
Dipodomys ordii ENSDORG000000160241 retrocopy
retro_dord_673,
Homo sapiens ENSG000001651193 retrocopies
retro_hsap_2323, retro_hsap_2674, retro_hsap_3385,
Loxodonta africana ENSLAFG000000265671 retrocopy
retro_lafr_809,
Macropus eugenii ENSMEUG000000069753 retrocopies
retro_meug_271, retro_meug_357, retro_meug_484,
Microcebus murinus ENSMICG000000157803 retrocopies
retro_mmur_1562, retro_mmur_235, retro_mmur_448,
Myotis lucifugus ENSMLUG000000058712 retrocopies
retro_mluc_128, retro_mluc_561,
Macaca mulatta ENSMMUG000000188711 retrocopy
retro_mmul_2111,
Monodelphis domestica ENSMODG000000084021 retrocopy
retro_mdom_1666,
Mus musculus ENSMUSG00000021546 2 retrocopies
retro_mmus_1131 , retro_mmus_2137,
Mus musculus ENSMUSG000000568511 retrocopy
retro_mmus_274,
Nomascus leucogenys ENSNLEG000000034863 retrocopies
retro_nleu_1178, retro_nleu_1815, retro_nleu_973,
Otolemur garnettii ENSOGAG000000074783 retrocopies
retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii ENSPPYG000000193273 retrocopies
retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii ENSSHAG000000171091 retrocopy
retro_shar_820,
Sus scrofa ENSSSCG000000227601 retrocopy
retro_sscr_437,
Tupaia belangeri ENSTBEG000000012891 retrocopy
retro_tbel_2491,
Tarsius syrichta ENSTSYG000000011963 retrocopies
retro_tsyr_1664, retro_tsyr_1796, retro_tsyr_2149,
Tursiops truncatus ENSTTRG000000049061 retrocopy
retro_ttru_1622,
Tursiops truncatus ENSTTRG000000166937 retrocopies
retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,




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