RetrogeneDB ID:

retro_mmus_2982

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:7:140890886..140892077(+)
Located in intron of:ENSMUSG00000025487
Retrocopy
information
Ensembl ID:ENSMUSG00000083396
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Dnaja1
Ensembl ID:ENSMUSG00000028410
Aliases:Dnaja1, Hsj2, Nedd7
Description:DnaJ (Hsp40) homolog, subfamily A, member 1 [Source:MGI Symbol;Acc:MGI:1270129]


Retrocopy-Parental alignment summary:






>retro_mmus_2982
ATGGTGAAAGAAACCGCTTACTACGATGTTTTGGGGGTAAAACCCAATGCCACCCAGGAAGAATTGAAAAAGGAATATAG
AAAATTGGCCTTGAAGTACCACCCTGATAAGAATCCAAATGAAGGAGAAAAGTTTAAACAGATTTCTCAAGCTTATGAAG
TTCTTGCTGATTCCAAAAAAAGGGAACTATATGATAAAGGAGGGGAGCAGGCGATTAAAGAGGGCGGAGCAGGTGGTGGT
TTTGGCTCACCCATGGATATCTTTGATATGTTCTTTGGAGGAGGAGGAAGAATGCAAAGAGAAAGGAGAGGTAAAAATGT
TGTTCATCAGCTCTCAGTGACCTTAGAAGACTTATATAATGGTGCAACAAGAAAACTGGCTCTGCAAAAGAATGTGATTT
GTGACAAATGTGAAGGCCGAGGTGGTAAGAAAGGAGCAGTAGAGTGCTGTCCCAACTGCCGGGGGACAGGTATGCAGATA
AGGATTCATCAGATTGGACCAGGAATGGTTCAGCAAATTCAGTCAGTGTGCATGGAGTGCCAGGGTCATGGAGAACGCAT
CAGTCCAAAAGACAGATGTAAAAGCTGCAATGGAAGAAAAATAGTTCGAGAGAAGAAAATTTTAGAAGTTCATATTGATA
AAGGCATGAAAGATGGTCAGAAGATAACATTCCACGGTGAAGGAGACCAAGAACCAGGACTGGAGCCAGGAGATATTATC
ATTGTGTTAGATCAGAAGGACCATGCTGTTTTTACAAGGCGAGGAGAAGACCTTTTTATGTGTATGGACATACAGCTGAT
TGAAGCATTGTGCGGCTTCCAAAAGCCACTATCTACTCTTGACAACCGAACCATAGTCATCACCTCTCATCCAGGTCAGA
TTGTCAAGCATGGGGATATAAAATGTGTGCTAAATGAAGGTATGCCAATATACCGTCAGCCATATGAAAAGGGACGTCTA
ATCATTGAGTTTAAGGTAAACTTTCCTGAAAATGGCTTTCTCTCTCCTGATAAACTCTCTTTGCTGGAAAAACTCCTTCC
TGAAAGGAAGGAAGTAGAAGAGACTGATGAAATGGATCAGGTAGAACTGGTGGACTTTGATCCAAATCAGGAAAGACGGC
GTCATTATAATGGAGAAGCGTATGAGGATGATGAACATCACCCCAGAGGTGGCGTTCAGTGTCAGACCTCT

ORF - retro_mmus_2982 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.74 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLADSKKRELYDKGGEQ
MVKET.YYDVLGVKPNATQEELKK.YRKLALKYHPDKNPNEGEKFKQISQAYEVLADSKKRELYDKGGEQ
RetrocopyMVKETAYYDVLGVKPNATQEELKKEYRKLALKYHPDKNPNEGEKFKQISQAYEVLADSKKRELYDKGGEQ
ParentalAIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGR
AIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGR
RetrocopyAIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGR
ParentalGGKKGAVECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEV
GGKKGAVECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEV
RetrocopyGGKKGAVECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEV
ParentalHIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTL
HIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQL.EALCGFQKP.STL
RetrocopyHIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLIEALCGFQKPLSTL
ParentalDNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERK
DNRTIVITSHPGQIVKHGDIKCVLNEGMPIYR.PYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERK
RetrocopyDNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRQPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERK
ParentalEVEETDEMDQVELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS
EVEETDEMDQVELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS
RetrocopyEVEETDEMDQVELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS

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 .40 RPM 103 .33 RPM
SRP007412_cerebellum 0 .69 RPM 81 .46 RPM
SRP007412_heart 0 .34 RPM 33 .68 RPM
SRP007412_kidney 0 .79 RPM 125 .45 RPM
SRP007412_liver 0 .38 RPM 146 .46 RPM
SRP007412_testis 0 .37 RPM 69 .93 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_2982 was not detected

EST - click to see more details

8 EST(s) were mapped to retro_mmus_2982 retrocopy
EST ID Start End Identity Match Mis-match Score
AA414938 140891099 140891502 99.3 399 3 395
BP766104 140891059 140891567 100 508 0 508
BQ042982 140891023 140891574 100 551 0 551
BQ264795 140891107 140891609 98.7 495 7 488
BY367714 140891081 140891474 99 389 4 385
CA555148 140891054 140891480 99.8 425 1 424
CD543486 140891048 140891566 100 518 0 518
CN714919 140891061 140891553 99.8 491 1 490

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_130459363 libraries 469 libraries 221 libraries 16 libraries 3 libraries

The graphical summary, for retro_mmus_2982 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_2982 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2982 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 83 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000075894 retrocopies
retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Canis familiaris ENSCAFG0000000181823 retrocopies
retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Callithrix jacchus ENSCJAG0000000802210 retrocopies
retro_cjac_1645, retro_cjac_1777, retro_cjac_2015, retro_cjac_2120, retro_cjac_2730, retro_cjac_2731, retro_cjac_2763, retro_cjac_3037, retro_cjac_3762, retro_cjac_887,
Cavia porcellus ENSCPOG000000004626 retrocopies
retro_cpor_1456, retro_cpor_225, retro_cpor_386, retro_cpor_396, retro_cpor_561, retro_cpor_781,
Gorilla gorilla ENSGGOG000000070303 retrocopies
retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Myotis lucifugus ENSMLUG000000160867 retrocopies
retro_mluc_1245, retro_mluc_1485, retro_mluc_1737, retro_mluc_1878, retro_mluc_2062, retro_mluc_2579, retro_mluc_576,
Monodelphis domestica ENSMODG000000033847 retrocopies
retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Mus musculus ENSMUSG00000028410 3 retrocopies
retro_mmus_2561, retro_mmus_2982 , retro_mmus_3507,
Mus musculus ENSMUSG000000322851 retrocopy
retro_mmus_2632,
Procavia capensis ENSPCAG000000122732 retrocopies
retro_pcap_184, retro_pcap_220,
Pteropus vampyrus ENSPVAG000000114701 retrocopy
retro_pvam_672,
Rattus norvegicus ENSRNOG000000070292 retrocopies
retro_rnor_2208, retro_rnor_608,
Sorex araneus ENSSARG000000013735 retrocopies
retro_sara_280, retro_sara_312, retro_sara_671, retro_sara_741, retro_sara_748,
Sarcophilus harrisii ENSSHAG000000123661 retrocopy
retro_shar_762,
Ictidomys tridecemlineatus ENSSTOG000000052004 retrocopies
retro_itri_265, retro_itri_303, retro_itri_378, retro_itri_809,
Tarsius syrichta ENSTSYG000000013294 retrocopies
retro_tsyr_110, retro_tsyr_1384, retro_tsyr_1921, retro_tsyr_57,


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