RetrogeneDB ID:

retro_mdom_1917

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:8:129758706..129759865(-)
Located in intron of:ENSMODG00000016726
Retrocopy
information
Ensembl ID:ENSMODG00000016729
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_1917
ATCCCAGCTTTTTCCCTTTTGAAAACACTAAGAATAATGTCCTTACATCAATTTTTACTAGAGCCAATCACCTGCCATGC
TTGGAACAGAGACCATACCCATTCTTACTTGGAGATTGCCCTTAGCCCTAATAATCATGAAGTCCACATCTACAAGAAGA
ATGGGAAACAATGGATGAAAGCCCATGAACTGAAGGAACACAATGGACACATCACAGGTATTGCCTGGGCTCCCAAGAGC
AATCGCATTTTAACTTGTGGGGCAGACTGCAATGCCTATGTCTGGAGTCAGAAAGATGGAATCTGGAAGCCAACCTTGGT
GATATTGAGGATTAATCGTGCAGCTACCTTTGTGAAATGGTCTCCCTTAGAGAATAAATTTGCTGTAGGTAGTGGAGCTC
AACTGATTTCTGTGTGCTACTTTGAGTCTGAAAATGACTGGTGGGTGAGCAAACACATAAAAAAGCCAATTCATTCTACT
GTCCTTAGTTTGGACTGGCACCCCAACAATGTTTTGCTGGCTGCTGGATCTTGTGACTTCAAATGCAGAGTATATTCTGC
CTACATTAAAGAAGTTGATGAAAAACCAGCCAATTCTCCATGGGGTACCAAGATGCCTTTTGGTCAGCTGATGTCAGGAG
TTTGGTGGTACTGAAAGTGGTGGTTGGGTCCATGGGGTCAGTTTCTCTGCCAGTGGGAACCGCCTCGCTTGGGTCAGCCA
TGATAGTACTGTATCAGTTGTTGATGCCTCTAAAAACATGATGGTTTCACAGCTGAAAACAGAGTTCCTCCCATTCCTGA
GTGTGTCATTTGTCTCTGAGAATAGTGTGGTGGCTGCTGGCCATGACTGCTGCCTGATGCTGTTTAATTATGATGATTGT
GGCCCCTTGACCTTCATCTCCAAATTAGACATTCCAAAAGAGAGCACTCAGTGCAACATCTCTGCCATGGAATGCTTCTG
CAACATGGACAAGAGAGCCACAACCGAGGATCACAACACTGCTCTAGACACACTACACCAAAACAGCATCGCCCAAATGT
CTATTTATGAAGTGGACAAGCAAGAATGCTGCAAATTTTGCACCACTGGCATTGATGGAGCTATGACAATTTGGGATTCC
AAGACTTTAAAGTCTTTGATCCAGGGACTATGACTCATG

ORF - retro_mdom_1917 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.92 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalISAFSLLKTLRIMSLHQFLLEPITCHAWNRDRT----QIALSPNNHEVHIYKKNGNQWMKAHELKEHNGH
I.AFSLLKTLRIMSLHQFLLEPITCHAWNRD.T.....IALSPNNHEVHIYKKNG.QWMKAHELKEHNGH
RetrocopyIPAFSLLKTLRIMSLHQFLLEPITCHAWNRDHTHSYLEIALSPNNHEVHIYKKNGKQWMKAHELKEHNGH
ParentalITGIDWAPKSDRIVTCGADRNAYVWSQKDGIWKPTLVILRINRAATFVKWSPLENKFAVGSGARLISVCY
ITGI.WAPKS.RI.TCGAD.NAYVWSQKDGIWKPTLVILRINRAATFVKWSPLENKFAVGSGA.LISVCY
RetrocopyITGIAWAPKSNRILTCGADCNAYVWSQKDGIWKPTLVILRINRAATFVKWSPLENKFAVGSGAQLISVCY
ParentalFESENDWWVSKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKPASTPWGTKMPFGQL
FESENDWWVSKHIKKPI.STVLSLDWHPNNVLLAAGSCDFKCRV.SAYIKEVDEKPA..PWGTKMPFGQL
RetrocopyFESENDWWVSKHIKKPIHSTVLSLDWHPNNVLLAAGSCDFKCRVYSAYIKEVDEKPANSPWGTKMPFGQL
ParentalMS-EFGGTGSGGWVHGVSFSASGNRLAWVSHDSTVSVADASKNMMVSQLKTEFLPLLSVSFVSENSVVAA
MS.EFGGT.SGGWVHGVSFSASGNRLAWVSHDSTVSV.DASKNMMVSQLKTEFLP.LSVSFVSENSVVAA
RetrocopyMS>EFGGTESGGWVHGVSFSASGNRLAWVSHDSTVSVVDASKNMMVSQLKTEFLPFLSVSFVSENSVVAA
ParentalGHDCCPMLFNYDDRGPLTFVSKLDIPKQSIQRNISAMERFRNMDKRATTEDRNTALDTLHQNSITQVSIY
GHDCC.MLFNYDD.GPLTF.SKLDIPK.S.Q.NISAME.F.NMDKRATTED.NTALDTLHQNSI.Q.SIY
RetrocopyGHDCCLMLFNYDDCGPLTFISKLDIPKESTQCNISAMECFCNMDKRATTEDHNTALDTLHQNSIAQMSIY
ParentalEVDKQDCRKFCTTGIDGAMTIWDFKTLESSIQGLRIM
EVDKQ.C.KFCTTGIDGAMTIWD.KTL.S.IQGL..M
RetrocopyEVDKQECCKFCTTGIDGAMTIWDSKTLKSLIQGL*LM

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_1917 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1917 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,