RetrogeneDB ID:

retro_mmus_294

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:1:9450655..9451743(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Hibch
Ensembl ID:ENSMUSG00000041426
Aliases:Hibch, 2610509I15Rik, AI648812
Description:3-hydroxyisobutyryl-Coenzyme A hydrolase [Source:MGI Symbol;Acc:MGI:1923792]


Retrocopy-Parental alignment summary:






>retro_mmus_294
AGTGTTATTCTGCAACAACTGAGAATGTCCATGCACACAGAAGCTGCAGAAGTGCTACTGGAGAGGAGAGGCTGTGCAGG
GGTCATAACACTCAACAGACTCAATGCACTGAGTCTGAATATGATCCAGCAGATCTATCCACAGCTAAAGAAGTGGAAAC
AAGACCTTGACACATTCCTGATCATCATAAAGGGAGCCTGAGGAAAGGCCTTTTGTGCTGGAGTGGACATCAAAGCACTC
TCAGAAGCTAAAAAAGCGAGACAGAATTGGACTCATGATGTATTCAGAGAAGAATACATCCTGAACAATGCAATTGCATC
TTGTCAGAAACCATATGTTGCCCTTATTGATGGAATCACCATGTTTGGGGAAGTTGGTCTTTCAGTTCATGGTCATTTCC
GAGTGGCTACAGAAAGGTCTCTCTTTGCTATGCCAGAAACAGGAATAGGACTATTTCCTGATGTGGGTAGAGGTTATTTC
CTGCCAACATTTCAAGGAAAACTGGGTTACTTCCTTGCACTGACAGGACACAGATTAAAAGGAAGAGATGTGCACAGAGC
GGGAATTGACACACACTTTGTAGATTCAGAAAAGTTGCATGTGTTGGAGGAGGAGCTGTTAGCCTTAAACTCACCTCCAG
CTGAGGATGTTGCAGGTGTCTTAGAAAACTATCATGCCAAGTCCAAGATGGATCAAGACAAATCTTTATATTTGAGGAAC
ACATGGGCAAAATAAACAGTTGTTTTTCAGCCAATACCATGGAACAGATAATTGAAAACTTATGGCAAAATGGATCACCT
TTTGCCATAGAATAGATGAAGGTAATTAATAAAATGTCTCTGACATCACTAAAGATCACACGAAGGCAGCTCATGGAGGG
TTCTTCAAAGACCTTGCAAGAGGTACTGACCATGGAATATCGGTTAACTCAAGCATGTATGGAAGGTTATAACTTTCATG
AAGGTGTTAGAGTTGTTATCATTGACAAAGACCAGACTTCAACATGGAAACCAGCCAGTCTAAAAGATTTTACTGATAAA
GATTTGAATAGTTATTTTAAATCTCTGGGAAGCACTGATTTGAAATTC

ORF - retro_mmus_294 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.19 %
Parental protein coverage: 95.06 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSVILQHLRMSMHTEAAEVLLERRGCGGVITLNRPKFLNALSLNMIRQIYPQLKTWEQDPDTFLIIIKGAG
SVILQ.LRMSMHTEAAEVLLERRGC.GVITLNR...LNALSLNMI.QIYPQLK.W.QD.DTFLIIIKGA.
RetrocopySVILQQLRMSMHTEAAEVLLERRGCAGVITLNR---LNALSLNMIQQIYPQLKKWKQDLDTFLIIIKGA*
ParentalGKAFCAGGDIKALSEAKKARQNLTQDLFREEYILNNAIASCQKPYVALIDGITMGGGVGLSVHGQFRVAT
GKAFCAG.DIKALSEAKKARQN.T.D.FREEYILNNAIASCQKPYVALIDGITM.G.VGLSVHG.FRVAT
RetrocopyGKAFCAGVDIKALSEAKKARQNWTHDVFREEYILNNAIASCQKPYVALIDGITMFGEVGLSVHGHFRVAT
ParentalERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGYRLKGRDVHRAGIATHFVDSEKLRVLEEELL
ERSLFAMPETGIGLFPDVG.GYFLP..QGKLGYFLALTG.RLKGRDVHRAGI.THFVDSEKL.VLEEELL
RetrocopyERSLFAMPETGIGLFPDVGRGYFLPTFQGKLGYFLALTGHRLKGRDVHRAGIDTHFVDSEKLHVLEEELL
ParentalALKSPSAEDVAGVLESYHAKSKMDQDKSI-IFEEHMDKINSCFSANTVEQIIENLRQDGSPFAIEQMKVI
AL.SP.AEDVAGVLE.YHAKSKMDQDKS..IFEEHM.KINSCFSANT.EQIIENL.Q.GSPFAIE.MKVI
RetrocopyALNSPPAEDVAGVLENYHAKSKMDQDKSL<IFEEHMGKINSCFSANTMEQIIENLWQNGSPFAIE*MKVI
ParentalNKMSPTSLKITLRQLMEGSSKTLQEVLIMEYRITQACMEGHDFHEGVRAVLIDKDQTPKWKPANLKDVTD
NKMS.TSLKIT.RQLMEGSSKTLQEVL.MEYR.TQACMEG..FHEGVR.V.IDKDQT..WKPA.LKD.TD
RetrocopyNKMSLTSLKITRRQLMEGSSKTLQEVLTMEYRLTQACMEGYNFHEGVRVVIIDKDQTSTWKPASLKDFTD
ParentalEDLNSYFKSLGSSDLKF
.DLNSYFKSLGS.DLKF
RetrocopyKDLNSYFKSLGSTDLKF

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 0 .00 RPM 10 .54 RPM
SRP007412_cerebellum 0 .00 RPM 12 .90 RPM
SRP007412_heart 0 .00 RPM 49 .19 RPM
SRP007412_kidney 0 .02 RPM 44 .95 RPM
SRP007412_liver 0 .00 RPM 53 .63 RPM
SRP007412_testis 0 .05 RPM 4 .85 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_294 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_294 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_77718862 libraries192 libraries16 libraries1 library1 library

The graphical summary, for retro_mmus_294 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_294 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_294 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Felis catus ENSFCAG000000033411 retrocopy
retro_fcat_890,
Homo sapiens ENSG000001981301 retrocopy
retro_hsap_3285,
Gorilla gorilla ENSGGOG000000049881 retrocopy
retro_ggor_1317,
Macaca mulatta ENSMMUG000000072831 retrocopy
retro_mmul_2062,
Mus musculus ENSMUSG00000041426 1 retrocopy
retro_mmus_294 ,
Nomascus leucogenys ENSNLEG000000066461 retrocopy
retro_nleu_1351,
Pongo abelii ENSPPYG000000130212 retrocopies
retro_pabe_2714, retro_pabe_2827,
Pan troglodytes ENSPTRG000000127411 retrocopy
retro_ptro_2222,
Tupaia belangeri ENSTBEG000000041321 retrocopy
retro_tbel_3398,


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