RetrogeneDB ID:

retro_mmus_2164

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:3:59431740..59433345(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Pabpc1
Ensembl ID:ENSMUSG00000022283
Aliases:Pabpc1, PABP, Pabp1, PabpI, Pabpl1, ePAB
Description:poly(A) binding protein, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:1349722]


Retrocopy-Parental alignment summary:






>retro_mmus_2164
GGAGTAGGCAACATATTCATTAAAAATTTGGACAAATCCATCGACAATAAAGCACTATATGATACGTTTTCTGCGTTTGG
TAACATCCTTTCATGTAAAGTGGTTTGTGATGAAAATGGCTCCAAGGGCTACGGATTTGTTCATTTTGAAACACAGGAAG
CAGCTGAAAGAGCTATTGAAAAAATGAATGGGATGCTTCTAAATGACCGTAAAGTGTGTGTTGGACGATTTACATCTCAG
AAGGAACGAGAAGCAGAACTTGGAGCCAGGGCAAAGGAGTTCACCAATGTTTACATCAAGAACTTCGGAGAAGACATGGA
TGATGAGCGCCTTAAGGAACTCTTTGGCAAGTTTGGGCCTGCCTTAAGTGTGAAAGTAATGACAGATGAAAGGGAAAATA
CAAAGGATTTGGATTTGTAAGCTTTGAAAGGCATGAAGATGCGCAGAAAGCTGTTGATGAGATGAATGGAAAGGAAATCA
ATGGAAAACAGATTTATGTTGGTCGAGCTCAGAAAAAAAGTGGAACGGCAGATGGAACTTAAGCACAAATTTGAGCAGAT
GAAGCAAGATAGGATCACCAGATATCAGGGTGTGAACCTTTATGTGAAAAATCTTGATGACGGTGTTGATGATGAACATC
TCCGGAAGGAGTTCTCTCCGTTTGGTACAATCACCAGTGCAAAAGTAATGATGGAGGGTGGGTACAGCAAAGGGTTTGGT
TTTGTATGTTTTTCATCCCCCGAAGAAGCCACTAAAGCAGTTACAGAGATGAATGGTAGAATTGTGGACACAAAGCCTCT
GTATGTAGCTTTAGCTCAACGCAAAGAAGAACGCCAGGCTCACCTCACTAACCAGTATATGCAGAGCATGGCAAGTGTAC
GAGCTGTGCCCAACCCCGTGATCAACCCCTACCAACCAGCACCTCCTTCAGGTTACTTCATGGCAGCTATCCCACAGACT
CAGAACCATGCTACATACTATCCTCCTAGCCAAATTGCTCAACTAAGATCAAGTCCTCGCTGGACTGCTCAGGGTGCCAG
ACCTCATCCATTCCAGAATATGTCTGGTGCTATCCGTCCAGCTACTCCTAGACCACCATTTAATACAATGAGACCAGCTT
CCTCACAGGTTCCACGAGTCATGTCAACACAGCGTGTTGCTAACACATCAACACAGACAATGGGTACACGTCTTGCAGCA
GCTGCAGCCACTCCTGCTGTCCGCACCATTCCCCAGTAAAAATACCCTGAGAGAGTCCGCCATCCCCAGCAACATCTTAA
TGCACAGCCACAAGTTACCATGCAACAGCCTGCTGTTCATATGCAAGGTCAAGAACCTTTAACTGCTTCCATGTTGGCAT
CTGCGTCCCAGCAAGAGCAGAAGCAAATGTTGGGGGAATAGCTGTTTCCTCTTATTCAAGCCGTGCACCCTTCTCTTGCT
GGTAAAATGCTGTTGGAGATTGATAACTCAGAATTACTTCACATGCTTGAGTCTCCAGAGTCTCTCCACTCAAAAGTTGA
TGAAGCTGTAGCTGTACTACGAGCCCACCAAGTGAAAGAGGCTGCCCAGAAAGCAGTGAACAGTGCCACTGGTGTCCCAA
CTGTC

ORF - retro_mmus_2164 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.25 %
Parental protein coverage: 84.91 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR
GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR
RetrocopyGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR
ParentalKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDE-SGKSKGFGF
KV.VGRF.S.KEREAELGARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDE..GK.KGFGF
RetrocopyKVCVGRFTSQKEREAELGARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDE<KGKYKGFGF
ParentalVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQ-KKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDG
VSFERHEDAQKAVDEMNGKE.NGKQIYVGRAQ.KKVERQ.ELK.KFEQMKQDRITRYQGVNLYVKNLDDG
RetrocopyVSFERHEDAQKAVDEMNGKEINGKQIYVGRAQ>KKVERQMELKHKFEQMKQDRITRYQGVNLYVKNLDDG
ParentalIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEER
.DDE.LRKEFSPFGTITSAKVMMEGG.SKGFGFVCFSSPEEATKAVTEMNGRIV.TKPLYVALAQRKEER
RetrocopyVDDEHLRKEFSPFGTITSAKVMMEGGYSKGFGFVCFSSPEEATKAVTEMNGRIVDTKPLYVALAQRKEER
ParentalQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTAQGARP
QAHLTNQYMQ.MASVRAVPNPVINPYQPAPPSGYFMAAIPQTQN.A.YYPPSQIAQLR.SPRWTAQGARP
RetrocopyQAHLTNQYMQSMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNHATYYPPSQIAQLRSSPRWTAQGARP
ParentalHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRVANTSTQTMGPRPAAAAAAATPAVRTVPQYKYA
HPFQNM.GAIRPA.PRPPF.TMRPASSQVPRVMSTQRVANTSTQTMG.R...AAAAATPAVRT.PQ.KY.
RetrocopyHPFQNMSGAIRPATPRPPFNTMRPASSQVPRVMSTQRVANTSTQTMGTR--LAAAAATPAVRTIPQ*KYP
ParentalAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPSLAGKITGM
..VR.PQQHLNAQPQVTMQQPAVH.QGQEPLTASMLASA..QEQKQMLGE.LFPLIQA.HPSLAGK...M
RetrocopyERVRHPQQHLNAQPQVTMQQPAVHMQGQEPLTASMLASASQQEQKQMLGE*LFPLIQAVHPSLAGK---M
ParentalLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAAQKAVNSATGVPTV
LLEIDNSELLHMLESPESL.SKVDEAVAVL.AHQ.KEAAQKAVNSATGVPTV
RetrocopyLLEIDNSELLHMLESPESLHSKVDEAVAVLRAHQVKEAAQKAVNSATGVPTV

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 .09 RPM 112 .73 RPM
SRP007412_cerebellum 0 .22 RPM 87 .88 RPM
SRP007412_heart 0 .06 RPM 95 .29 RPM
SRP007412_kidney 0 .35 RPM 201 .93 RPM
SRP007412_liver 0 .14 RPM 223 .25 RPM
SRP007412_testis 2 .97 RPM 1753 .45 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2164 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2164 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_95375633 libraries311 libraries123 libraries5 libraries0 libraries
TSS #2 TSS_95376702 libraries303 libraries67 libraries0 libraries0 libraries
TSS #3 TSS_95377209 libraries382 libraries449 libraries24 libraries8 libraries
TSS #4 TSS_95378409 libraries503 libraries153 libraries3 libraries4 libraries

The graphical summary, for retro_mmus_2164 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_2164 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2164 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000003481 retrocopy
retro_amel_1650,
Choloepus hoffmanni ENSCHOG000000081781 retrocopy
retro_chof_2531,
Callithrix jacchus ENSCJAG000000158335 retrocopies
retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus ENSCPOG000000129171 retrocopy
retro_cpor_1324,
Dasypus novemcinctus ENSDNOG000000087182 retrocopies
retro_dnov_1530, retro_dnov_2259,
Felis catus ENSFCAG000000018741 retrocopy
retro_fcat_1927,
Homo sapiens ENSG000000707561 retrocopy
retro_hsap_88,
Gorilla gorilla ENSGGOG000000067851 retrocopy
retro_ggor_1986,
Myotis lucifugus ENSMLUG000000122451 retrocopy
retro_mluc_579,
Macaca mulatta ENSMMUG000000177862 retrocopies
retro_mmul_1462, retro_mmul_895,
Monodelphis domestica ENSMODG000000062224 retrocopies
retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus ENSMUSG000000112577 retrocopies
retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Mus musculus ENSMUSG00000022283 2 retrocopies
retro_mmus_102, retro_mmus_2164 ,
Mus musculus ENSMUSG000000400431 retrocopy
retro_mmus_1530,
Nomascus leucogenys ENSNLEG000000031423 retrocopies
retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus ENSOCUG000000043541 retrocopy
retro_ocun_13,
Pongo abelii ENSPPYG000000187903 retrocopies
retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus ENSPVAG000000166402 retrocopies
retro_pvam_10, retro_pvam_855,
Rattus norvegicus ENSRNOG000000086393 retrocopies
retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii ENSSHAG000000112671 retrocopy
retro_shar_24,
Sus scrofa ENSSSCG000000060632 retrocopies
retro_sscr_1153, retro_sscr_1205,
Ictidomys tridecemlineatus ENSSTOG000000163952 retrocopies
retro_itri_139, retro_itri_48,
Tarsius syrichta ENSTSYG000000042292 retrocopies
retro_tsyr_1743, retro_tsyr_273,
Tursiops truncatus ENSTTRG000000046892 retrocopies
retro_ttru_1050, retro_ttru_1812,
Vicugna pacos ENSVPAG000000038654 retrocopies
retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,




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