RetrogeneDB ID:

retro_mmus_2160

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:3:57362355..57363371(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Aldoa
Ensembl ID:ENSMUSG00000030695
Aliases:Aldoa, Aldo-1, Aldo1
Description:aldolase A, fructose-bisphosphate [Source:MGI Symbol;Acc:MGI:87994]


Retrocopy-Parental alignment summary:






>retro_mmus_2160
ACCACGCCCTACTCATACTCAGAACTGACCCCAGAGCAGAGGGAGCTGTCTGACATCGCTCACCAAATTGTGGCTCCAGG
CAAGGGCATCCTGGCTACAGACGAGTCCACTGGAAGCATTGATAAGCCCCTGCAGTCCATTGGCACCGAGAACACCGAGG
AGAACAGGCACTTCTACTGTCAACTGCTGCTTACTGCTGATGACCGTGTGAATCCCTGCATTTGGGGGTGGGGGTTTGAT
CCTCACGAGACTCTGTACCAGAAGGCAGATGATGGACGACCCTTCCCCCAAGTTATCAAGTCCAAGGGTGGTGTTGTGGG
CATTAAGGTAGATAAGAGTGTGGTGCCCCTGGCAGGAACCAATGGTGAGACCACTACCCAAGATCTGGATGACCTGTTTG
ACCGCTGTGCCCAGTATAAGAAGGATGGAGCCAACTTTGCCAAGTGGCGCTGTGTATTAAAGATTGGGGAACATACTCCC
TTAGCCCTTGCCATCATGGAAAATGCCAATGTTCTGACCCGTTATGCCAGCATCTGCCAGCAGAATAGCATTGTACCCAT
TGTGGAGCCTTAAATTCTCCCTGATGGGGACCATGACTTGAAGCGCCGCCAGCTATGACTGAGAAGGTACTGGCGGCTGT
CTACAAGGCTCTGAGCGACCACCATGTCTATCTGGAAGGCACATTTTTGAAGCCCAACGTGGTCACCCCTGGCCATGCTT
GCACCCAGAAATTTTCCAATGAGGAGATTGCCATGGCAACGGTCACAGCACTTCGTTGCATAGTGCCCCCTGCAGTCCCT
GGGGTCACTTTCCTGTCTGGAGGGCAGAGTGAGGAAGAGGCATCCATCAACCTCAAGGCTATCAACAAGTGTCCCCTACT
GAAGCAATGGGCCTTGACTTTCTCCTAGTGCCGAGCCCTGTAGGCCTCTGCTCTAAAGACCTGGGGTGGGAAGAAGGAGA
ACCTGAAGAGTTCAGGAGCCCCAGAGGAGTACATCAAGTGAGCCCTGGACAACAGC

ORF - retro_mmus_2160 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.34 %
Parental protein coverage: 80.62 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalTMPHPYPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDR
T.P..Y..LTPEQ..ELSDIAH.IVAPGKGILA.DESTGSI.K.LQSIGTENTEENR.FY.QLLLTADDR
RetrocopyTTPYSYSELTPEQR-ELSDIAHQIVAPGKGILATDESTGSIDKPLQSIGTENTEENRHFYCQLLLTADDR
ParentalVNPCI-GGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQY
VNPCI.G.....HETLYQKADDGRPFPQVIKSKGGVVGIKVDK.VVPLAGTNGETTTQ.LD.L..RCAQY
RetrocopyVNPCIWGWGFDPHETLYQKADDGRPFPQVIKSKGGVVGIKVDKSVVPLAGTNGETTTQDLDDLFDRCAQY
ParentalKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQY-VTE
KKDGA.FAKWRCVLKIGEHTP.ALAIMENANVL.RYASICQQN.IVPIVEP.ILPDGDHDLKR.Q...TE
RetrocopyKKDGANFAKWRCVLKIGEHTPLALAIMENANVLTRYASICQQNSIVPIVEP*ILPDGDHDLKRRQL<MTE
ParentalKVLAAVYKALSDHHVYLEGTLLKPNMVTPGHACTQKFSNEEIAMATVTALRRTVPPAVTGVTFLSGGQSE
KVLAAVYKALSDHHVYLEGT.LKPN.VTPGHACTQKFSNEEIAMATVTALR..VPPAV.GVTFLSGGQSE
RetrocopyKVLAAVYKALSDHHVYLEGTFLKPNVVTPGHACTQKFSNEEIAMATVTALRCIVPPAVPGVTFLSGGQSE
ParentalEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKA--AQEEYIKRALANS
EEASINL.AINKCPLLK.WALTFS..RAL.ASALK.WGGKKENLK...A.EEYIK.AL.NS
RetrocopyEEASINLKAINKCPLLKQWALTFS*CRAL*ASALKTWGGKKENLKSSGAPEEYIK*ALDNS

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 .35 RPM 1035 .35 RPM
SRP007412_cerebellum 0 .26 RPM 1045 .41 RPM
SRP007412_heart 1 .18 RPM 2044 .01 RPM
SRP007412_kidney 0 .42 RPM 1259 .68 RPM
SRP007412_liver 0 .38 RPM 87 .00 RPM
SRP007412_testis 0 .14 RPM 329 .87 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2160 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2160 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_95221384 libraries453 libraries227 libraries6 libraries2 libraries

The graphical summary, for retro_mmus_2160 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_2160 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2160 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000082212 retrocopies
retro_cfam_190, retro_cfam_631,
Callithrix jacchus ENSCJAG000000068741 retrocopy
retro_cjac_1803,
Cavia porcellus ENSCPOG000000074341 retrocopy
retro_cpor_951,
Echinops telfairi ENSETEG000000192301 retrocopy
retro_etel_20,
Homo sapiens ENSG000001499251 retrocopy
retro_hsap_740,
Gorilla gorilla ENSGGOG000000139791 retrocopy
retro_ggor_621,
Myotis lucifugus ENSMLUG000000112103 retrocopies
retro_mluc_1172, retro_mluc_2634, retro_mluc_808,
Macaca mulatta ENSMMUG000000009831 retrocopy
retro_mmul_2596,
Monodelphis domestica ENSMODG000000156964 retrocopies
retro_mdom_1236, retro_mdom_1356, retro_mdom_528, retro_mdom_96,
Mus musculus ENSMUSG00000030695 3 retrocopies
retro_mmus_2160 , retro_mmus_42, retro_mmus_90,
Nomascus leucogenys ENSNLEG000000021521 retrocopy
retro_nleu_133,
Oryctolagus cuniculus ENSOCUG000000063291 retrocopy
retro_ocun_1550,
Ochotona princeps ENSOPRG000000097601 retrocopy
retro_opri_914,
Pongo abelii ENSPPYG000000072441 retrocopy
retro_pabe_636,
Pan troglodytes ENSPTRG000000079831 retrocopy
retro_ptro_526,
Rattus norvegicus ENSRNOG000000236477 retrocopies
retro_rnor_1343, retro_rnor_1541, retro_rnor_1796, retro_rnor_1807, retro_rnor_226, retro_rnor_2791, retro_rnor_536,


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