RetrogeneDB ID:

retro_mdom_442

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:1:557351708..557352465(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000012060
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CNN3
Ensembl ID:ENSMODG00000004326
Aliases:None
Description:calponin 3, acidic [Source:HGNC Symbol;Acc:2157]


Retrocopy-Parental alignment summary:






>retro_mdom_442
ATGACCCACTTCAACAAGGGCCCTTCTTATGGGCTCTCAGCCGAAGTCAAGAATAAGATTGCCTCCAAATATGACCATCA
GGCAGAGGAAGATCTTCGTAATTGGATAGAAGAAGTTACAGGCTTGAGCATTGGGACAAACTTTCCGCTGGGCTTAAAAG
ATGGCATCATACTCTGTGAACTTATAAACAAGCTACAGCCAGGTTCAGTGAAAAAAGTTAATGAATCTTCATTAAACTGG
CTTCAGTTGGAGAACATTGGTAACTTTATTAAAGCCATTCAAGCTTATGGTATGAAGCCACATGACATCTTTGAAGCAAA
TGATCTCTTTGAAAATGGAAACATGACCCAAGTTCAGACTACATTGGTAGCTTTAGCAGGTCTGGCTAAAACAAAAGGAT
TCCATACGACAATTGACATTGGTGTCAAATATGCAGAAAAGCAAGCGAGGCATTTTTAATGAAGGAAAACTAAAAGCTGG
ACAAAGTGTGATTGGCCTGCAGATGGGAACCAACAAATGTGCCAGCCAGGCAGGAATGACTGCTTATGGGACTAGGAGGC
ATCTTTATGATCCCAAAATGCAAACTGACAAGCCTTTTGACCAGACAACAATTAGTCTGCAGATGGGAACTAACAAAGGA
GCCAGTCAGGCTGGAATGTTAGCACCTGGTACCAGAAGAGACATCTATGATCAGCAGCTAACATTACAACCAGTGAACAA
CTCAAGGATTTCGTTACAGATGGCGACCACTAGATTG

ORF - retro_mdom_442 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.02 %
Parental protein coverage: 76.51 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMTHFNKGPSYGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGLSIGTNFQLGLKDGIILCELINKLQPGSV
MTHFNKGPSYGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGLSIGTNF.LGLKDGIILCELINKLQPGSV
RetrocopyMTHFNKGPSYGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGLSIGTNFPLGLKDGIILCELINKLQPGSV
ParentalKKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTIDI
KKVNESSLNW.QLENIGNFIKAIQAYG..............NGNMTQVQTTLVALAGLAKTKGFHTTIDI
RetrocopyKKVNESSLNWLQLENIGNFIKAIQAYGXXXXXXXXXXXXXXNGNMTQVQTTLVALAGLAKTKGFHTTIDI
ParentalGVKYAEKQARR-FDEGKLKAGQSVIGLQAIMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQ
GVKYAEKQAR..F.EGKLKAGQSVIGLQ..MGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQ
RetrocopyGVKYAEKQARH>FNEGKLKAGQSVIGLQ--MGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQ
ParentalMGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKV
MGTNKGASQAGMLAPGTRRDIYDQ.LTLQPV.NS.ISLQM.T...
RetrocopyMGTNKGASQAGMLAPGTRRDIYDQQLTLQPVNNSRISLQMATTRL

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 .51 RPM 0 .00 RPM
SRP007412_cerebellum 9 .47 RPM 0 .00 RPM
SRP007412_heart 2 .19 RPM 0 .00 RPM
SRP007412_kidney 35 .55 RPM 0 .00 RPM
SRP007412_liver 16 .62 RPM 0 .00 RPM
SRP007412_testis 3 .14 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_442 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_442 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 19 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000167071 retrocopy
retro_amel_1412,
Bos taurus ENSBTAG000000203451 retrocopy
retro_btau_1211,
Callithrix jacchus ENSCJAG000000181283 retrocopies
retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Dasypus novemcinctus ENSDNOG000000128833 retrocopies
retro_dnov_223, retro_dnov_403, retro_dnov_815,
Equus caballus ENSECAG000000201881 retrocopy
retro_ecab_655,
Echinops telfairi ENSETEG000000100951 retrocopy
retro_etel_638,
Homo sapiens ENSG000001175191 retrocopy
retro_hsap_3419,
Gorilla gorilla ENSGGOG000000138701 retrocopy
retro_ggor_2312,
Macropus eugenii ENSMEUG000000029212 retrocopies
retro_meug_2020, retro_meug_42,
Macaca mulatta ENSMMUG000000016901 retrocopy
retro_mmul_1747,
Monodelphis domestica ENSMODG00000004326 1 retrocopy
retro_mdom_442 ,
Monodelphis domestica ENSMODG000000100321 retrocopy
retro_mdom_1178,
Mustela putorius furoENSMPUG000000033321 retrocopy
retro_mputfur_896,
Mus musculus ENSMUSG000000539312 retrocopies
retro_mmus_1052, retro_mmus_2544,
Nomascus leucogenys ENSNLEG000000112075 retrocopies
retro_nleu_122, retro_nleu_1342, retro_nleu_2698, retro_nleu_480, retro_nleu_668,
Pan troglodytes ENSPTRG0000000097915 retrocopies
retro_ptro_1061, retro_ptro_1149, retro_ptro_1247, retro_ptro_1447, retro_ptro_1505, retro_ptro_1554, retro_ptro_1871, retro_ptro_215, retro_ptro_2323, retro_ptro_2377, retro_ptro_2831, retro_ptro_2894, retro_ptro_3007, retro_ptro_483, retro_ptro_653,
Sarcophilus harrisii ENSSHAG000000026701 retrocopy
retro_shar_567,
Tarsius syrichta ENSTSYG000000107492 retrocopies
retro_tsyr_1458, retro_tsyr_1907,
Vicugna pacos ENSVPAG000000048892 retrocopies
retro_vpac_190, retro_vpac_449,


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