RetrogeneDB ID:

retro_mdom_1360

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:4:133560071..133561078(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000001115
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ARPC1A
Ensembl ID:ENSMODG00000001303
Aliases:None
Description:actin related protein 2/3 complex, subunit 1A, 41kDa [Source:HGNC Symbol;Acc:703]


Retrocopy-Parental alignment summary:






>retro_mdom_1360
AAGAAGAATGGGAACCAATGGATGAAAGCCCATGAACTGAAAGAGCACAATGGACACATCACAGGTATTGACTGGGCTCC
CAAGAGCGATCATATTGTAACATGTGGGGCAGACCGCAATGCCTATGTCTGGAGTCAGAAAGATGGAATCTGGAAGTCAG
CCTTGGTGATCTTGAGGATTAATCATGCAGCCACCTTTGTGAAATGGTCTCCCCTGGAGAATAAATTTGCTGTAGGCAGT
GGAGCTCGGCTGATTTCTGTGTGCTACTTTGAGTCTGAAAATGACTGGTGGGTGAGCAAACACATAAAAAAGCCAATTCG
TTCTACTGTCCTTAGTTTGGACTGGCACCCCAACAATGTTTTTGCTGGCTGCTGGATCTTATGACTTCAAATGCAGAGTA
TTTTCTGCCCACATTAAAGAAGTTGATGAAAAACCAGCCAGTACTCCATGGGGTACCAAGATGCCTTTTGGTCAGCTGAT
GTCAAGAGTTTTGTGGTACTGGAAATGGTGGTTGGGTCCATGGGTTCAGTTTCTCTGCCAGTGGGAACCGCCTGACTCGG
GTCAGCCAGGATAGTACTGTATCAGTTGCTGATGCCTCTAAAAACATGATGGTTTCACAGCTAAAAACAGAGTTCCTCCC
ACTCCTGAGTGTGTCATTTGTTTCTGAGAATAGCGTGGTGGCTGCTGGCCATGACTGCTACCCGATGCTGTTTAATTATG
ATGATCGTGGCTCCTTGACCTTCATCTCCAAATTACACAATCCAAAACAGAGCATTCAGCGCAACATCTCTGCCATGGAA
TGCTTCCACAACATGGACAAGAGAGCCACAACCGAGGATCACAACACTGCTCTAGACACACTACACCAGAACAGTATCAC
CCAAGTGTCTATTTATGAAATGGACAAGCAAGACTGCCGCAAATTTTGCACCACTGGCATTGATGGAGCTATGACAATTT
GGGATTTCAAGACTTTAGAGTCTTCGATCCAGGGGCTACGAATCATG

ORF - retro_mdom_1360 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.18 %
Parental protein coverage: 87.7 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalKKNGNQWMKAHELKEHNGHITGIDWAPKSDRIVTCGADRNAYVWSQKDGIWKPTLVILRINRAATFVKWS
KKNGNQWMKAHELKEHNGHITGIDWAPKSD.IVTCGADRNAYVWSQKDGIWK..LVILRIN.AATFVKWS
RetrocopyKKNGNQWMKAHELKEHNGHITGIDWAPKSDHIVTCGADRNAYVWSQKDGIWKSALVILRINHAATFVKWS
ParentalPLENKFAVGSGARLISVCYFESENDWWVSKHIKKPIRSTVLSLDWHPNNV-LLAAGSCDFKCRVFSAYIK
PLENKFAVGSGARLISVCYFESENDWWVSKHIKKPIRSTVLSLDWHPNNV.LLAAGS.DFKCRVFSA.IK
RetrocopyPLENKFAVGSGARLISVCYFESENDWWVSKHIKKPIRSTVLSLDWHPNNV>LLAAGSYDFKCRVFSAHIK
ParentalEVDEKPASTPWGTKMPFGQLMS-EFGGTGSGGWVHGVSFSASGNRLAWVSHDSTVSVADASKNMMVSQLK
EVDEKPASTPWGTKMPFGQLMS.EF.GTG.GGWVHG.SFSASGNRL..VS.DSTVSVADASKNMMVSQLK
RetrocopyEVDEKPASTPWGTKMPFGQLMS>EFCGTGNGGWVHGFSFSASGNRLTRVSQDSTVSVADASKNMMVSQLK
ParentalTEFLPLLSVSFVSENSVVAAGHDCCPMLFNYDDRGPLTFVSKLDIPKQSIQRNISAMERFRNMDKRATTE
TEFLPLLSVSFVSENSVVAAGHDC.PMLFNYDDRG.LTF.SKL..PKQSIQRNISAME.F.NMDKRATTE
RetrocopyTEFLPLLSVSFVSENSVVAAGHDCYPMLFNYDDRGSLTFISKLHNPKQSIQRNISAMECFHNMDKRATTE
ParentalDRNTALDTLHQNSITQVSIYEVDKQDCRKFCTTGIDGAMTIWDFKTLESSIQGLRIM
D.NTALDTLHQNSITQVSIYE.DKQDCRKFCTTGIDGAMTIWDFKTLESSIQGLRIM
RetrocopyDHNTALDTLHQNSITQVSIYEMDKQDCRKFCTTGIDGAMTIWDFKTLESSIQGLRIM

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_1360 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1360 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 24 parental genes, and 64 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063221 retrocopy
retro_amel_1431,
Bos taurus ENSBTAG000000042421 retrocopy
retro_btau_1486,
Callithrix jacchus ENSCJAG000000158593 retrocopies
retro_cjac_2141, retro_cjac_2165, retro_cjac_2263,
Cavia porcellus ENSCPOG000000017772 retrocopies
retro_cpor_452, retro_cpor_981,
Dasypus novemcinctus ENSDNOG000000059845 retrocopies
retro_dnov_1615, retro_dnov_1839, retro_dnov_1966, retro_dnov_2257, retro_dnov_941,
Dipodomys ordii ENSDORG000000160591 retrocopy
retro_dord_593,
Equus caballus ENSECAG000000164671 retrocopy
retro_ecab_185,
Homo sapiens ENSG000002416852 retrocopies
retro_hsap_2010, retro_hsap_3191,
Loxodonta africana ENSLAFG000000140241 retrocopy
retro_lafr_1006,
Macropus eugenii ENSMEUG000000056098 retrocopies
retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Myotis lucifugus ENSMLUG000000109121 retrocopy
retro_mluc_1432,
Macaca mulatta ENSMMUG000000193422 retrocopies
retro_mmul_1383, retro_mmul_2012,
Monodelphis domestica ENSMODG00000001303 9 retrocopies
retro_mdom_1360 , retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917, retro_mdom_686, retro_mdom_699, retro_mdom_808,
Mus musculus ENSMUSG000000296211 retrocopy
retro_mmus_1373,
Nomascus leucogenys ENSNLEG000000108522 retrocopies
retro_nleu_1663, retro_nleu_2069,
Oryctolagus cuniculus ENSOCUG000000039441 retrocopy
retro_ocun_1130,
Otolemur garnettii ENSOGAG000000108706 retrocopies
retro_ogar_1547, retro_ogar_2690, retro_ogar_2697, retro_ogar_381, retro_ogar_610, retro_ogar_656,
Pongo abelii ENSPPYG000000258164 retrocopies
retro_pabe_1647, retro_pabe_1648, retro_pabe_2537, retro_pabe_2647,
Pan troglodytes ENSPTRG000000338192 retrocopies
retro_ptro_1340, retro_ptro_2253,
Sarcophilus harrisii ENSSHAG000000106732 retrocopies
retro_shar_180, retro_shar_727,
Sus scrofa ENSSSCG000000076091 retrocopy
retro_sscr_387,
Ictidomys tridecemlineatus ENSSTOG000000016601 retrocopy
retro_itri_1834,
Tupaia belangeri ENSTBEG000000113813 retrocopies
retro_tbel_1237, retro_tbel_1241, retro_tbel_82,
Tursiops truncatus ENSTTRG000000030024 retrocopies
retro_ttru_1621, retro_ttru_1838, retro_ttru_575, retro_ttru_853,


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