RetrogeneDB ID:

retro_mdom_89

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:218186402..218187530(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000023940
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTG1
Ensembl ID:ENSMODG00000002647
Aliases:None
Description:actin, gamma 1 [Source:HGNC Symbol;Acc:144]


Retrocopy-Parental alignment summary:






>retro_mdom_89
ATGGATGATGATATTGCTGCGCTCGTTGTTGACAATGGATCCGGTATGTGCAAAGCTGGCTTTGCAGGAGATGATGCCCC
TCGGGCTGTCTTCCCTTCCATTGTGGGGCGCCCCAGACATCAGGGTGTGATGGTGGGTATGGGCCAGAAAGACAGCTATG
TGGGGGATGAGGCCCAGAGCAAGAGAGGTATTCTGACCCTGAAGTACCCCATTGAACACGGTATTGTCACCAACTGGGAT
GACATGGAGAAGATCTGGCATCATACTTTCTACAATGAGCTCCGTGTGGCCCCTGAAGAGCACCCTGTACTGCTCACAGA
AGCCCCCCTGAACCCCAAAGCCAACAGAGAAAAGATGACACAGATCATGTTTGAGACCTTCAACACCCCAGCTATGTACG
TTGCCATCCAGGCTGTGCTGTCCCTGTATGCCTCTGGTCGTACCACTGGTATCGTGATGGACTCCGGTGTTGGTGTGACC
CACACTGTGCCCATCTATGAAGGTTATGCCCTTCCCCATGCCATTCTCCGTCTGGATCTGGCTGGCCGTGATCTGACGGA
TTACCTCATGAAGATCCTGACCGAGAGAGGGTACAGTTTCACCACCACAGCTGAGAGGGAAATCGTGCGTGACATCAAGG
AGAAGCTGTGTTACGTGGCCCTCGACTTTGAGCAGGAGATGGCCACTGCTGCATCCAGCTCTTCTCTGGAGAAGAGCTAC
GAGCTCCCTGATGGTCAGGTTATCACCATTGGCAATGAGAGGTTCCGGTGCCCAGAGGCTCTCTTCCAGCCATCTTTCTT
AGGCATGGAGTCCTGTGGAATCCATGAAACTACTTTCAACTCAATCATGAAGTGTGATGTTGACATCCGTAAGGATTTGT
ATGCCAATACCGTATTGTCTGGTGGTACCACCATGTACCCAGGCATTGCTGACAGGATGCAGAAGGAGATTACAGCCCTA
GCCCCCAGCACAATGAAAATCAAGATCATTGCCCCACCTGAGCGCAAATACTCTGTCTGGATTGGAGGCTCCATCCTGGC
CTCCCTCTCCACCTTCCAACAGATGTGGATCAGTAAGCAGGAGTATGATGAATCTGGGCCTTCCATTGTCCACCGCAAAT
GCTTCTAA

ORF - retro_mdom_89 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.67 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
M...IAALV.DNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
RetrocopyMDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
ParentalIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
RetrocopyIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
ParentalSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
SLYASGRTTGIVMDSG.GVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
RetrocopySLYASGRTTGIVMDSGVGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
ParentalDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
DIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
RetrocopyDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
ParentalSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS
SIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS
RetrocopySIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS
ParentalTFQQMWISKQEYDESGPSIVHRKCF
TFQQMWISKQEYDESGPSIVHRKCF
RetrocopyTFQQMWISKQEYDESGPSIVHRKCF

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_89 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_89 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 24 parental genes, and 65 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000152383 retrocopies
retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca ENSAMEG000000160151 retrocopy
retro_amel_929,
Callithrix jacchus ENSCJAG000000028853 retrocopies
retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus ENSCPOG000000121011 retrocopy
retro_cpor_361,
Equus caballus ENSECAG000000186001 retrocopy
retro_ecab_98,
Felis catus ENSFCAG000000264342 retrocopies
retro_fcat_257, retro_fcat_377,
Homo sapiens ENSG0000018400910 retrocopies
retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus ENSGALG000000287491 retrocopy
retro_ggal_6,
Gorilla gorilla ENSGGOG000000140436 retrocopies
retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Monodelphis domestica ENSMODG00000002647 3 retrocopies
retro_mdom_187, retro_mdom_59, retro_mdom_89 ,
Mustela putorius furoENSMPUG000000116101 retrocopy
retro_mputfur_279,
Mus musculus ENSMUSG000000628257 retrocopies
retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys ENSNLEG000000155063 retrocopies
retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Oryctolagus cuniculus ENSOCUG000000058671 retrocopy
retro_ocun_720,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pongo abelii ENSPPYG0000000873511 retrocopies
retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pelodiscus sinensis ENSPSIG000000021022 retrocopies
retro_psin_25, retro_psin_4,
Rattus norvegicus ENSRNOG000000367011 retrocopy
retro_rnor_715,
Sorex araneus ENSSARG000000121971 retrocopy
retro_sara_267,
Sus scrofa ENSSSCG000000283551 retrocopy
retro_sscr_389,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Tupaia belangeri ENSTBEG000000107811 retrocopy
retro_tbel_422,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,


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