RetrogeneDB ID:

retro_mdom_1476

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:5:220103599..220104288(+)
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:ENSMODG00000020456
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_1476
GAGGAAAAACTGTGGGAGCAGAAACACTGAAGAAAAAAAAGAGTACACTGTTCTTTATCAGACACTTTTTGATAAGAGAA
GTGAAATCATCAATGCAATTTATGAACCGACAGAGGAAGAATGTGAATAGAAATTGGATGAAGACAACATTTCAGAGGAA
ATGAAAGAGAAGACTAAGCATGAAGAGGAGGGGAAAAAAAGAAAAAGAATTCTGTAAAGAAATTCCTGAATTTTGGCTGA
CTTTTTAAAAAATGTTGACTTGCTCAGTGATATGGTTCGAGAACATGATGAACCTATTCTGAAGCATTTGAAAGATATTA
AAGTGAAGTTCTCAGATGCTGGACTGCCTATGAGTTTTATGTTAGAATTTCACTTTGAACCCAACAAATATTTCACAAAT
GAGGTGTTGATGAAGACACATCGTATGTTCTCAGAGCCAGATGATTCTGATCCCTTCTCCTTTGATGGACCAGAAATTAT
GAGTTGCACAGAGTGTCAGGTAGACTGGAAAAATGGGAAAAATGTTACTTTGAAAACTATTAAGAAGCAAAAACAAGAGA
TGTGGCACCGTTCGAACTGTGACAAAAACAGTTTCCAATGATTCTTTTTTCAATTTCTTTTCTCTTCCTGAAGTTCCTGA
GAGTGGAGACCTGGATGATGATGCAGAGGCTATCCTTGCTGCAGACTTC

ORF - retro_mdom_1476 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.12 %
Parental protein coverage: 59.34 %
Number of stop codons detected: 1
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalEAKFYEEVH-ALERKYAVLYQPLFDKRSEIINAIYEPTEEECEWKPDDDEEISEMKEKAKLEEE-KKDEE
E.K..E..H......Y.VLYQ.LFDKRSEIINAIYEPTEEECE.K.D.D..ISE........EE......
RetrocopyEEKLWEQKH>EXXXEYTVLYQTLFDKRSEIINAIYEPTEEECE*KLDEDN-ISEEMKEKTKHEE>RXXXX
ParentalKEDPKGIPEFWLTV-FKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQPMSFTLEFHFEPNEYFTNEVL
.E..K.IPEFWLT...KNVDLLSDMV.EHDEPILKHLKDIKVKFSDAG.PMSF.LEFHFEPN.YFTNEVL
RetrocopyXEFCKEIPEFWLTF<LKNVDLLSDMVREHDEPILKHLKDIKVKFSDAGLPMSFMLEFHFEPNKYFTNEVL
ParentalMKTYRMRSEPDDSDPFSFDGPEIMSCTGCQVDWKKGKNVTLKTIKK-KQKHKGRGTVRTVTKTVSNDSFF
MKT.RM.SEPDDSDPFSFDGPEIMSCT.CQVDWK.GKNVTLKTIKK.K.K..G..TVRTVTKTVSNDSFF
RetrocopyMKTHRMFSEPDDSDPFSFDGPEIMSCTECQVDWKNGKNVTLKTIKK>KNKRCG--TVRTVTKTVSNDSFF
ParentalNFFSPPEVPESGDLDDDAEAILAADF
NFFS.PEVPESGDLDDDAEAILAADF
RetrocopyNFFSLPEVPESGDLDDDAEAILAADF

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_1476 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1476 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 21 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000209088 retrocopies
retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Choloepus hoffmanni ENSCHOG000000032102 retrocopies
retro_chof_1095, retro_chof_2057,
Callithrix jacchus ENSCJAG000000011151 retrocopy
retro_cjac_534,
Felis catus ENSFCAG000000002791 retrocopy
retro_fcat_1037,
Homo sapiens ENSG000001871093 retrocopies
retro_hsap_1199, retro_hsap_2696, retro_hsap_833,
Gorilla gorilla ENSGGOG000000038833 retrocopies
retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Macropus eugenii ENSMEUG000000137022 retrocopies
retro_meug_1031, retro_meug_604,
Macaca mulatta ENSMMUG000000155831 retrocopy
retro_mmul_233,
Monodelphis domestica ENSMODG00000020456 4 retrocopies
retro_mdom_1476 , retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furoENSMPUG000000174741 retrocopy
retro_mputfur_505,
Mus musculus ENSMUSG000000587991 retrocopy
retro_mmus_263,
Nomascus leucogenys ENSNLEG000000046824 retrocopies
retro_nleu_1192, retro_nleu_2085, retro_nleu_265, retro_nleu_2766,
Oryctolagus cuniculus ENSOCUG000000138571 retrocopy
retro_ocun_834,
Otolemur garnettii ENSOGAG000000103194 retrocopies
retro_ogar_1278, retro_ogar_1281, retro_ogar_3357, retro_ogar_666,
Pongo abelii ENSPPYG000000047862 retrocopies
retro_pabe_2287, retro_pabe_999,
Pan troglodytes ENSPTRG000000052404 retrocopies
retro_ptro_1820, retro_ptro_582, retro_ptro_694, retro_ptro_819,
Pteropus vampyrus ENSPVAG000000160322 retrocopies
retro_pvam_1282, retro_pvam_306,
Rattus norvegicus ENSRNOG000000038901 retrocopy
retro_rnor_150,
Ictidomys tridecemlineatus ENSSTOG000000030462 retrocopies
retro_itri_1007, retro_itri_416,
Tursiops truncatus ENSTTRG000000170622 retrocopies
retro_ttru_160, retro_ttru_1921,
Vicugna pacos ENSVPAG000000072903 retrocopies
retro_vpac_435, retro_vpac_441, retro_vpac_601,


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