RetrogeneDB ID:

retro_mdom_1356

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:4:123515813..123516781(-)
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:ENSMODG00000015696
Aliases:None
Description:Fructose-bisphosphate aldolase [Source:UniProtKB/TrEMBL;Acc:F7E0Q7]


Retrocopy-Parental alignment summary:






>retro_mdom_1356
GCAGCTGCAATCCATCCCATCGGAACTGAGGACACAGAAGAAAATTACCGCCTTTATAGGCAGTTACTTCTGACAGCAGA
TGATCGAGTGAACAACTGCATTGGAGGTGTCATCCTTTTCCATGAGACGCTCTACCAGAAAACTGATGATGGTCGTCCCT
TTCCCAAAGGCATAAAGGGCAAGGGTGGTGTTGTGGGCATCAAGGTGGACAAAGGTGTAGTGCCCCTGGCAGGGACCAAT
GGGGAGAATACTACCCAAGGTCTGGATGGGCTAGCTGAGCGCTATGCCCAGTATAAGAAGGATGGGGCTGACTTTGCCAA
GTGGCGTTGTGTTCTGAAGATTGGGAAAAATACACCTCCACTTACCATCATGGACAATGCCAATGTGCTGGCCAGTTATG
CCAGCATTTGCCAGCAGAATGGCATTGTCCCCATTGTGGAGCCAGAGATCCTCCCTGATGGAGAACATGATCTGAAGTGT
TGCCAGTATGTCACCGAGAAGGTTCTGGCTGCTGTCTACAAAGCTTTGAGTGACCACCACATCTATCTGAGGGGACCTTG
CTGAAGCCTAACATGGTCACTCCTGGCCATGCTTGTACCCAGAAATATTCGCATGAGGAGCTTGCAATGGCAACTGTAAC
TGCCCTTCACCGGACTGTGCCTCCTGCAGTCACTGGTATCATCTTCCTGTCTGGGGGTCAGAGTGAGGAGGATGCTTCCA
TCAATCTCAATGCCATCAACACCTGCCTCTTGCACAAGCCATGGGCCCTGACCTTTTCTTGTGGCTGAGCCCTGCAGGCA
TCTGCCCTCAAGACCTGGGGTGGAAAGAAGGAAAATGTCTGGGCTGCCCAGGAGGAATATGTTAAGCAGGCCTTGGCTAA
TAGCCAGGCTGCTCAAGGCAAGTATACTCCATCTGGGAAGTCAGGAGCTGCAGCCAGCGAGTCCCTCTTTGTCTCTAACC
ATGCCTAC

ORF - retro_mdom_1356 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.69 %
Parental protein coverage: 89.01 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalAKRLQSIGTENTEENRRLYRQLLLTADDRVNSCIGGVILFHETLYQKADDGRPFPKVIKAKGGVVGIKVD
A.....IGTE.TEEN.RLYRQLLLTADDRVN.CIGGVILFHETLYQK.DDGRPFPK.IK.KGGVVGIKVD
RetrocopyAAAIHPIGTEDTEENYRLYRQLLLTADDRVNNCIGGVILFHETLYQKTDDGRPFPKGIKGKGGVVGIKVD
ParentalKGVVPLAGTNGETTTQGLDGLAERCAQYKKDGADFAKWRCVLKIGENTPSPLAIMENANVLARYASICQQ
KGVVPLAGTNGE.TTQGLDGLAER.AQYKKDGADFAKWRCVLKIG.NTP.PL.IM.NANVLA.YASICQQ
RetrocopyKGVVPLAGTNGENTTQGLDGLAERYAQYKKDGADFAKWRCVLKIGKNTP-PLTIMDNANVLASYASICQQ
ParentalNGIVPIVEPEILPDGEHDLKCCQYVTEKVLAAVYKALSDHHIYL-EGTLLKPNMVTPGHACTQKYSHEEI
NGIVPIVEPEILPDGEHDLKCCQYVTEKVLAAVYKALSDHHIYL.EGTLLKPNMVTPGHACTQKYSHEE.
RetrocopyNGIVPIVEPEILPDGEHDLKCCQYVTEKVLAAVYKALSDHHIYL<EGTLLKPNMVTPGHACTQKYSHEEL
ParentalAMATVTALRRTVPPAVTGITFLSGGQSEEDASINLNAINTCPLHKPWALTFSYGRALQASALKTWGGKKE
AMATVTAL.RTVPPAVTGI.FLSGGQSEEDASINLNAINTC.LHKPWALTFS.G.ALQASALKTWGGKKE
RetrocopyAMATVTALHRTVPPAVTGIIFLSGGQSEEDASINLNAINTCLLHKPWALTFSCG*ALQASALKTWGGKKE
ParentalNVQAAQEEYVKRALANSQAAQGKYTPSGKSGAAASESLFVSNHAY
NV.AAQEEYVK.ALANSQAAQGKYTPSGKSGAAASESLFVSNHAY
RetrocopyNVWAAQEEYVKQALANSQAAQGKYTPSGKSGAAASESLFVSNHAY

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_1356 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1356 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 17 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000082212 retrocopies
retro_cfam_190, retro_cfam_631,
Callithrix jacchus ENSCJAG000000068741 retrocopy
retro_cjac_1803,
Cavia porcellus ENSCPOG000000074341 retrocopy
retro_cpor_951,
Echinops telfairi ENSETEG000000192301 retrocopy
retro_etel_20,
Homo sapiens ENSG000001499251 retrocopy
retro_hsap_740,
Gorilla gorilla ENSGGOG000000139791 retrocopy
retro_ggor_621,
Myotis lucifugus ENSMLUG000000112103 retrocopies
retro_mluc_1172, retro_mluc_2634, retro_mluc_808,
Macaca mulatta ENSMMUG000000009831 retrocopy
retro_mmul_2596,
Monodelphis domestica ENSMODG000000144182 retrocopies
retro_mdom_1752, retro_mdom_393,
Monodelphis domestica ENSMODG00000015696 4 retrocopies
retro_mdom_1236, retro_mdom_1356 , retro_mdom_528, retro_mdom_96,
Mus musculus ENSMUSG000000306953 retrocopies
retro_mmus_2160, retro_mmus_42, retro_mmus_90,
Nomascus leucogenys ENSNLEG000000021521 retrocopy
retro_nleu_133,
Oryctolagus cuniculus ENSOCUG000000063291 retrocopy
retro_ocun_1550,
Ochotona princeps ENSOPRG000000097601 retrocopy
retro_opri_914,
Pongo abelii ENSPPYG000000072441 retrocopy
retro_pabe_636,
Pan troglodytes ENSPTRG000000079831 retrocopy
retro_ptro_526,
Rattus norvegicus ENSRNOG000000236477 retrocopies
retro_rnor_1343, retro_rnor_1541, retro_rnor_1796, retro_rnor_1807, retro_rnor_226, retro_rnor_2791, retro_rnor_536,


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