RetrogeneDB ID:

retro_mdom_1253

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:4:109332983..109333630(+)
Located in intron of:ENSMODG00000018639
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DNAJA1
Ensembl ID:ENSMODG00000003384
Aliases:None
Description:DnaJ (Hsp40) homolog, subfamily A, member 1 [Source:HGNC Symbol;Acc:5229]


Retrocopy-Parental alignment summary:






>retro_mdom_1253
GGGGAATGAATTAGCCCTAAAGATAAGTCTAAAAAGCTGTCATGGAAGGAAAATTTTTCTGAAGAAAAAAAATTCTAGAA
AGTTGATATTGACAAAAGCATGAAAGATGGTCAGAAAATAACATTCCATGGTGAAGGTGACCAGGAGCCAGGACTTTGAG
CCAGGAGATATTATCATTGCTTTGGATCAGTAGGACAATCCAATATTTACATGTCAGGGTGAGGACCTTTTCATGTGCAT
GGATATTCAGTTGGTTGAAGCATTGTGTGGTTTTTAGAAACCAACATCAATTCTTGCTAGTAGAACTATAGTCATTACTT
CTCATCTTGGTCAGATTGTCAAACATGGAGATATCAAATGAGTACTGAATGAAGGCATGCCTATTTATCACTGACCTTAT
GAGAAAGGAATTCTAATCATTGAATTTAAGGTAAATTTCCCAGAGAATGGCTTTCTTTCATCCGATAAGCTATTTTTATT
GGAAAAGTTACTGCTTGAAAGAAAGGAAGGAGAGGAGACTGGAAAAAATGGATCAGGTAGAATTGGTAGACTTTGAGCCA
TCTCCAGAAGGAAGGTGCCATTACAATGGGTAAGTTTATGAGGGTGATGAGCATCATCCCAGAGGTGGTGTTCAGTGTCA
AACCTCT

ORF - retro_mdom_1253 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.26 %
Parental protein coverage: 53.63 %
Number of stop codons detected: 7
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGERISPKDRCKSCNGRKIVREKKIL-EVHIDKGMKDGQKITFHGEGDQEPGL-EPGDIIIVLDQKDNPIF
GE.ISPKD..K.........E......V.IDK.MKDGQKITFHGEGDQEPGL.EPGDIII.LDQ.DNPIF
RetrocopyGE*ISPKDKSKKLSWKENFSEXXXF*KVDIDKSMKDGQKITFHGEGDQEPGL>EPGDIIIALDQ*DNPIF
ParentalTRRGEDLFMCMDIQLVEALCGFQKPISTLDSRTIVITSHPGQIVKHGDIKCVLNEGMPIYRRPYEKGILI
T..GEDLFMCMDIQLVEALCGF.KP.S.L.SRTIVITSH.GQIVKHGDIK.VLNEGMPIY..PYEKGILI
RetrocopyTCQGEDLFMCMDIQLVEALCGF*KPTSILASRTIVITSHLGQIVKHGDIK*VLNEGMPIYH*PYEKGILI
ParentalIEFKVNFPENGFLSSDKLSLLEKLLPERKEVEET-EEMDQVELVDFDPSQERRRHYNGEAYEDDEHHPRG
IEFKVNFPENGFLSSDKL.LLEKLL.ERKE.EET.E.MDQVELVDF.PS.E.R.HYNG..YE.DEHHPRG
RetrocopyIEFKVNFPENGFLSSDKLFLLEKLLLERKEGEET>EKMDQVELVDFEPSPEGRCHYNG*VYEGDEHHPRG
ParentalGVQCQTS
GVQCQTS
RetrocopyGVQCQTS

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 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_1253 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1253 was not experimentally validated.

Retrocopy orthology:
Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 32 parental genes, and 169 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000075894 retrocopies
retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Bos taurus ENSBTAG000000162656 retrocopies
retro_btau_1440, retro_btau_1599, retro_btau_1800, retro_btau_1826, retro_btau_574, retro_btau_828,
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,
Choloepus hoffmanni ENSCHOG000000006319 retrocopies
retro_chof_1760, retro_chof_186, retro_chof_2020, retro_chof_2541, retro_chof_2694, retro_chof_287, retro_chof_417, retro_chof_498, retro_chof_946,
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,
Dasypus novemcinctus ENSDNOG000000183423 retrocopies
retro_dnov_1139, retro_dnov_640, retro_dnov_884,
Echinops telfairi ENSETEG000000169846 retrocopies
retro_etel_1015, retro_etel_1454, retro_etel_1751, retro_etel_219, retro_etel_482, retro_etel_623,
Felis catus ENSFCAG000000087295 retrocopies
retro_fcat_1241, retro_fcat_1407, retro_fcat_1502, retro_fcat_1984, retro_fcat_811,
Homo sapiens ENSG000000860614 retrocopies
retro_hsap_2331, retro_hsap_2569, retro_hsap_3647, retro_hsap_4889,
Gorilla gorilla ENSGGOG000000070303 retrocopies
retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Loxodonta africana ENSLAFG000000015272 retrocopies
retro_lafr_1019, retro_lafr_936,
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,
Macaca mulatta ENSMMUG000000077406 retrocopies
retro_mmul_1313, retro_mmul_1802, retro_mmul_2477, retro_mmul_2482, retro_mmul_2625, retro_mmul_400,
Monodelphis domestica ENSMODG00000003384 7 retrocopies
retro_mdom_1140, retro_mdom_1253 , retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Mustela putorius furoENSMPUG000000042312 retrocopies
retro_mputfur_1543, retro_mputfur_487,
Mus musculus ENSMUSG000000284103 retrocopies
retro_mmus_2561, retro_mmus_2982, retro_mmus_3507,
Nomascus leucogenys ENSNLEG000000052684 retrocopies
retro_nleu_1255, retro_nleu_2550, retro_nleu_2793, retro_nleu_509,
Oryctolagus cuniculus ENSOCUG000000048332 retrocopies
retro_ocun_516, retro_ocun_70,
Procavia capensis ENSPCAG000000122732 retrocopies
retro_pcap_184, retro_pcap_220,
Pongo abelii ENSPPYG000000191414 retrocopies
retro_pabe_1892, retro_pabe_2111, retro_pabe_2559, retro_pabe_2994,
Pan troglodytes ENSPTRG000000208524 retrocopies
retro_ptro_1499, retro_ptro_1705, retro_ptro_177, retro_ptro_2472,
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,