RetrogeneDB ID:

retro_mdom_706

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:165237860..165238737(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000020738
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_706
AGTTACTTTTCATCATGTTCATTCCATCTAAGCTCAGTCATTATGTCAGGTTCAAATGGTACTGATGAGAATTCTCACAA
GGCTCGGACATCACCGTATCCAGGTTCAAAAGTTGAACATAGTCAAGTACTCAATGAGAAGGTGGGCTGATTTGTTGAGT
GGCAGGAGTATAATCCTGTGGAATATACTGCAGTCTCTGTCTTGACTGGACCCATGTGGGCAGATCCACAGATCAGTGAA
AGAAATTTTTCTCCTAAGTTTCATAAAAAGGATGGACGTGTTGAACGAAAGAGTCAGAATGGTTTGTATGAGATTGAAAA
TGGTCAACCTAGAAATCCAGCAGGTTGGACAGGATTGGTAGGCCGGGGACTTTTGGAACATTGGGGCCAAAACCATGCTG
CAGATCTCATTATTACTATGTGGAAAAAGGACAACAGTGGAAATAAAGTCATTCACCCTCATTCTGGGGAAAATATCTTA
CAATTTATAGAAATCAAGAGGAAAGACTGTGAAGAATGGGCAATCCCAGGGGAGATAGTGGGTCCAGGAGAGAAAATCAA
TGCTACCTTGAAATGAGAGTTTGGTGAAGAAGCTATGAACTCCTTACAGAAATCCACTGCTGAGAAGCAGGAGATGGAGG
AGCAGTTGCACAAACTCTTCAATCAAGAACATTTAGTGGTTTATTAAGGATATGTGGATGATCCTCGAAATACTGATAAT
GCCATGGATGGAGACGGAAGCTGTGAATTATCATCATGAAACAGGTGAGACAATGGATAATTTGGCTCTGGAATCAGGAG
ATGATGCTGGGACAGTCATATGGGTGGACATGAGATATAAACTAAAGCTTTATGCCAGCCATTCCCAGTTCATCAAA

ORF - retro_mdom_706 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.39 %
Parental protein coverage: 84.68 %
Number of stop codons detected: 3
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalSCFSSRSFHLSSVIMSGSNGADENSHNKARTSPYPGSKVERSQVPNEKVGWLVEWQEYNPVEYTAVSVLA
S.FSS.SFHLSSVIMSGSNG.DENSH.KARTSPYPGSKVE.SQV.NEKVG..VEWQEYNPVEYTAVSVL.
RetrocopySYFSSCSFHLSSVIMSGSNGTDENSH-KARTSPYPGSKVEHSQVLNEKVG*FVEWQEYNPVEYTAVSVLT
ParentalGPMWADPQISERNFSPKFNEKDGHVERKSQNGLYEIENGRPRNPAGRTGLVGRGLLGRWGPNHAADPIIT
GPMWADPQISERNFSPKF..KDG.VERKSQNGLYEIENG.PRNPAG.TGLVGRGLL..WG.NHAAD.IIT
RetrocopyGPMWADPQISERNFSPKFHKKDGRVERKSQNGLYEIENGQPRNPAGWTGLVGRGLLEHWGQNHAADLIIT
ParentalRWKRDSSGNKVIHPHSGKNILQFVAIKRKDCGEWAIPGGMVDPGEKISATLKREFGEEAMNSLQKSTAEK
.WK.D.SGNKVIHPHSG.NILQF..IKRKDC.EWAIPG..V.PGEKI.ATLK.EFGEEAMNSLQKSTAEK
RetrocopyMWKKDNSGNKVIHPHSGENILQFIEIKRKDCEEWAIPGEIVGPGEKINATLK*EFGEEAMNSLQKSTAEK
ParentalQEMEEQLHKLFSQEHLVVYKGYVDDPRNTDNA-WMETEAVNYHDETGETMDNLALEAGDDAGKVKWVDIS
QEMEEQLHKLF.QEHLVVY.GYVDDPRNTDNA.WMETEAVNYH.ETGETMDNLALE.GDDAG.V.WVD..
RetrocopyQEMEEQLHKLFNQEHLVVY*GYVDDPRNTDNA>WMETEAVNYHHETGETMDNLALESGDDAGTVIWVDMR
ParentalDKLKLYASHSQFIK
.KLKLYASHSQFIK
RetrocopyYKLKLYASHSQFIK

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_706 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_706 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 23 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000032441 retrocopy
retro_amel_612,
Bos taurus ENSBTAG000000113541 retrocopy
retro_btau_1112,
Canis familiaris ENSCAFG000000095291 retrocopy
retro_cfam_1271,
Callithrix jacchus ENSCJAG000000061591 retrocopy
retro_cjac_1047,
Ciona savignyi ENSCSAVG000000088371 retrocopy
retro_csav_15,
Equus caballus ENSECAG000000195561 retrocopy
retro_ecab_123,
Echinops telfairi ENSETEG000000191641 retrocopy
retro_etel_348,
Felis catus ENSFCAG000000033151 retrocopy
retro_fcat_1509,
Homo sapiens ENSG000001705021 retrocopy
retro_hsap_709,
Gorilla gorilla ENSGGOG000000147771 retrocopy
retro_ggor_602,
Loxodonta africana ENSLAFG000000113911 retrocopy
retro_lafr_224,
Macropus eugenii ENSMEUG000000121234 retrocopies
retro_meug_1072, retro_meug_1345, retro_meug_1758, retro_meug_2162,
Monodelphis domestica ENSMODG00000020738 2 retrocopies
retro_mdom_157, retro_mdom_706 ,
Mustela putorius furoENSMPUG000000022581 retrocopy
retro_mputfur_585,
Nomascus leucogenys ENSNLEG000000095201 retrocopy
retro_nleu_464,
Oryctolagus cuniculus ENSOCUG000000026702 retrocopies
retro_ocun_1045, retro_ocun_990,
Ochotona princeps ENSOPRG000000040551 retrocopy
retro_opri_1152,
Pongo abelii ENSPPYG000000149141 retrocopy
retro_pabe_613,
Pan troglodytes ENSPTRG000000162591 retrocopy
retro_ptro_506,
Pteropus vampyrus ENSPVAG000000048291 retrocopy
retro_pvam_475,
Sus scrofa ENSSSCG000000092231 retrocopy
retro_sscr_447,
Tursiops truncatus ENSTTRG000000042071 retrocopy
retro_ttru_1549,
Vicugna pacos ENSVPAG000000040121 retrocopy
retro_vpac_125,


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