RetrogeneDB ID:

retro_mdom_410

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:1:445970527..445971244(+)
Located in intron of:ENSMODG00000013219
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CAPNS1
Ensembl ID:ENSMODG00000014179
Aliases:None
Description:calpain, small subunit 1 [Source:HGNC Symbol;Acc:1481]


Retrocopy-Parental alignment summary:






>retro_mdom_410
CTCCTGGAAGGGGCTGAAAAAGGTCTTGGAGAAGCACTCGGAGGCGTCCGTGGTGGTGGAGGGCAAAAAGGAAAGGGGCA
TCTGGCAGACCTTGTTGGAGGAATTGTAAACCTCATCAGCGAGGCGTCTGCAGCTAAGTATACACCGGAACCACCACCCC
CTTACCAGCATTTTACAAACGTCGAAGCCAGTGAAAGTGATGAAGTTAGGCAGTTTCGTCGAGTCTTTTATCGGCTGGCG
GGAGATGACATGGAAGTGGGTCCTGCCGACCTGATGAACATTCTCAACAAAGTGATTTCCAAACACAGAGAATTGAATAC
AGATGGTTTTAGCCTTGACACTTGCCGGAGCATTGTAGCTGTCATGGATAGCGACGCAACAGGAAAACTAGGATTTGAGG
AATTTAAGTATCTGTGGAACAATATCAAGAAATGGCAATGTGTTTACAAGCAATATAACACCGACCATTCCACTTCCCTT
GGGGGAGGGCAGCTGAAGCAAGCTATTCAGGCAGCAGGCTTCCAGCTGCACGAGCAACTTTACCAAATGATTATTCGCAG
ATATACTGAAGAAGACGGAAGTATGGAATTTACTAGCTTTATTAGCTGCCTGGTACGTTTGGATGCTATGTTTCGCGCCT
TCAAGTCACTAGATGGAGATCGAGACGGCCAAGTTCAAGTAAATATTCAAGAATGGCTGGAACTTACTATGTATTCC

ORF - retro_mdom_410 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.95 %
Parental protein coverage: 90.46 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLLSGGGGGGGGA-GGGGGGGGGGGAGGAMGFLGGVISAISEA-AANYNPEPPPPRTHFSNIEANESEEVR
LL.G...G.G.A.GG..GGGG..G.G......GG....ISEA.AA.Y.PEPPPP..HF.N.EA.ES.EVR
RetrocopyLLEGAEKGLGEALGGVRGGGGQKGKGHLADLVGGIVNLISEASAAKYTPEPPPPYQHFTNVEASESDEVR
ParentalQFRRLFTQLAGDDMEVSASELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWN
QFRR.F..LAGDDMEV....LMNILNKV...H..L.TDGF..DTCRS.VAVMDSD.TGKLGFEEFKYLWN
RetrocopyQFRRVFYRLAGDDMEVGPADLMNILNKVISKHRELNTDGFSLDTCRSIVAVMDSDATGKLGFEEFKYLWN
ParentalNIKKWQAIYKQFDTDRSGTIGSNELPGAFEAAGFRLNPELYQMIIRRYSDEDGNMDFDNFISCLVRLDAM
NIKKWQ..YKQ..TD.S...G...L..A..AAGF.L...LYQMIIRRY..EDG.M.F..FISCLVRLDAM
RetrocopyNIKKWQCVYKQYNTDHSTSLGGGQLKQAIQAAGFQLHEQLYQMIIRRYTEEDGSMEFTSFISCLVRLDAM
ParentalFRAFKSLDKDGSGQIRVNIQEWLQLTMYS
FRAFKSLD.D..GQ..VNIQEWL.LTMYS
RetrocopyFRAFKSLDGDRDGQVQVNIQEWLELTMYS

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 7 .15 RPM 0 .00 RPM
SRP007412_cerebellum 15 .67 RPM 0 .00 RPM
SRP007412_heart 20 .73 RPM 0 .00 RPM
SRP007412_kidney 9 .22 RPM 0 .00 RPM
SRP007412_liver 2 .52 RPM 0 .00 RPM
SRP007412_testis 9 .23 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_410 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_410 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 31 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000005111 retrocopy
retro_acar_205,
Ailuropoda melanoleuca ENSAMEG000000010241 retrocopy
retro_amel_136,
Bos taurus ENSBTAG000000148722 retrocopies
retro_btau_1126, retro_btau_692,
Canis familiaris ENSCAFG000000313141 retrocopy
retro_cfam_942,
Callithrix jacchus ENSCJAG000000095941 retrocopy
retro_cjac_2940,
Cavia porcellus ENSCPOG000000001151 retrocopy
retro_cpor_1131,
Equus caballus ENSECAG000000122101 retrocopy
retro_ecab_707,
Echinops telfairi ENSETEG000000076502 retrocopies
retro_etel_1190, retro_etel_60,
Felis catus ENSFCAG000000141491 retrocopy
retro_fcat_1691,
Homo sapiens ENSG000001262471 retrocopy
retro_hsap_98,
Gorilla gorilla ENSGGOG000000036992 retrocopies
retro_ggor_1241, retro_ggor_263,
Microcebus murinus ENSMICG000000102551 retrocopy
retro_mmur_416,
Myotis lucifugus ENSMLUG000000249441 retrocopy
retro_mluc_2336,
Macaca mulatta ENSMMUG000000002492 retrocopies
retro_mmul_1334, retro_mmul_1567,
Monodelphis domestica ENSMODG00000014179 1 retrocopy
retro_mdom_410 ,
Mustela putorius furoENSMPUG000000056171 retrocopy
retro_mputfur_444,
Mus musculus ENSMUSG000000017941 retrocopy
retro_mmus_80,
Nomascus leucogenys ENSNLEG000000117122 retrocopies
retro_nleu_1328, retro_nleu_992,
Oryctolagus cuniculus ENSOCUG000000130931 retrocopy
retro_ocun_1095,
Otolemur garnettii ENSOGAG000000069921 retrocopy
retro_ogar_1956,
Ochotona princeps ENSOPRG000000165622 retrocopies
retro_opri_181, retro_opri_486,
Procavia capensis ENSPCAG000000063531 retrocopy
retro_pcap_165,
Pongo abelii ENSPPYG000000098982 retrocopies
retro_pabe_1359, retro_pabe_448,
Pelodiscus sinensis ENSPSIG000000127931 retrocopy
retro_psin_45,
Pan troglodytes ENSPTRG000000108872 retrocopies
retro_ptro_1112, retro_ptro_168,
Pteropus vampyrus ENSPVAG000000128853 retrocopies
retro_pvam_1375, retro_pvam_639, retro_pvam_737,
Rattus norvegicus ENSRNOG000000457472 retrocopies
retro_rnor_1447, retro_rnor_2145,
Sorex araneus ENSSARG000000042661 retrocopy
retro_sara_215,
Sus scrofa ENSSSCG000000301492 retrocopies
retro_sscr_495, retro_sscr_73,
Ictidomys tridecemlineatus ENSSTOG000000262351 retrocopy
retro_itri_342,
Vicugna pacos ENSVPAG000000080741 retrocopy
retro_vpac_64,




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