RetrogeneDB ID:

retro_ocun_1421

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:8:76668090..76669233(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTA2
Ensembl ID:ENSOCUG00000008193
Aliases:None
Description:actin, alpha 2, smooth muscle, aorta (ACTA2), mRNA [Source:RefSeq mRNA;Acc:NM_001101682]


Retrocopy-Parental alignment summary:






>retro_ocun_1421
GCTCCCACTCAGCTCACCATGGATGACGATATCACCGCGCTTGTGGTCGACAATGGCTCCGGCATGTGCAAGGCCGGCTT
CGCGGGCGACGATGCCCCCCGGGCTGTCTTCCTCTCCATAGTGGGGCGTCCGCGGCACCAGGGCGTGATGGTGGGCATGG
ACCATAAGGACTCGTACGTGGGCGACGAGGCCCAGAGCAAGCGTGGCATCCTGACGCTCAAGTACCCCATCGAGCACGGC
ATCGTGACCAACTAGGACGCCATGGAGAAGATCTGGCACCACACCTTCTACCACGAGCTGCGCGTGGCGCCCGAGGAGCA
CCCGGTGCTGCTGACCGAGGCCCCCCTGAACCCCAAGGCCAACCGCGAGAAGATGACCCAGATCATGTTCGAGACGTTCA
ACACGCTGGCCATGTACGTGGCCATCCAGGCTGTGCTGTCCCTGTACGCCTCTGGCCGCACCACGGGCATCGTGATGGAC
TCTGGCGACAGGGTCACCCACACGGTGCCCATCTACGAGGGCTACGCGCTGCCGCACACCATCCTGCGTCTGGACCTGGC
CGGCCGGGACCTGACTGACTACCTCATGAAGATCCTCACGGAGCGCGGCTACAGCTTCACCACCATGGCCGAGCGCGAGA
TCGTGCGGGACATCAAGGAGAAGCTGTGCTATTTGGCGCTGGACTTCGAGCAAGAGATGGCCACGGCCGCGAACTCCTCC
TCCCTGGAGAAGAGCTACGAGCCGCCCAACGGCCAGGTAATCACCATCTGCAACGAGCGCTTCCGCTGCCCCAGGCGCTG
TTCCAGCCCTCCTTCCTGGGCATGGAGTCGTGCGGCATCCACGAGACCACCTTCAATTCGATCATGAAGTGCGACGTGGA
CATCCGCAAGGACCTGTACGCCAACACGGTGCTGTCGGGCGGCACCACCATGTACCCTGGCATCGCGGACCGCATGCAGA
AGGAGATCACCGCCCTGGCGCCCAGCACCATGAAGATAAAGATCATCGCTCCCCCCCCAGCGCAAGTACTCGGTGTGGAT
CGGCGGCTCCATCCTGGCCTCGCTGTCCATGTTCCAGCAGATGTGGATCAGCAAGCAGGAGCACGATGAGTCGGGCCCCT
CCATCGTGCACCGCAAGTGTTTC

ORF - retro_ocun_1421 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.47 %
Parental protein coverage: 80.89 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalAAAAMCEEEDSTALVCDNGSGLCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGI
A........D.TALV.DNGSG.CKAGFAGDDAPRAVF.SIVGRPRHQGVMVGM..KDSYVGDEAQSKRGI
RetrocopyAPTQLTMDDDITALVVDNGSGMCKAGFAGDDAPRAVFLSIVGRPRHQGVMVGMDHKDSYVGDEAQSKRGI
ParentalLTLKYPIEHGIITNWDDMEKIWHHSFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYV
LTLKYPIEHGI.TN.D.MEKIWHH.FY.ELRVAPEEHP.LLTEAPLNPKANREKMTQIMFETFN..AMYV
RetrocopyLTLKYPIEHGIVTN*DAMEKIWHHTFYHELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTLAMYV
ParentalAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTA
AIQAVLSLYASGRTTGIV.DSGD.VTH.VPIYEGYALPH.I.RLDLAGRDLTDYLMKILTERGYSF.T.A
RetrocopyAIQAVLSLYASGRTTGIVMDSGDRVTHTVPIYEGYALPHTILRLDLAGRDLTDYLMKILTERGYSFTTMA
ParentalEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRC-PETLFQPSFIGMESAG
EREIVRDIKEKLCY.ALDFE.EMATAA.SSSLEKSYE.P.GQVITI.NERFRC.P..LFQPSF.GMES.G
RetrocopyEREIVRDIKEKLCYLALDFEQEMATAANSSSLEKSYEPPNGQVITICNERFRC<PQALFQPSFLGMESCG
ParentalIHETTYNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIA-PPERKYSVWIG
IHETT.NSIMKCD.DIRKDLYAN.VLSGGTTMYPGIADRMQKEITALAPSTMKIKIIA.PP.RKYSVWIG
RetrocopyIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIA>PPQRKYSVWIG
ParentalGSILASLSTFQQMWISKQEYDEAGPSIVHRKCF
GSILASLS.FQQMWISKQE.DE.GPSIVHRKCF
RetrocopyGSILASLSMFQQMWISKQEHDESGPSIVHRKCF

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
SRP017611_brain 35 .65 RPM 17 .99 RPM
SRP017611_kidney 31 .83 RPM 42 .77 RPM
SRP017611_liver 18 .19 RPM 22 .20 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_1421 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1421 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1421 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 14 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000007593 retrocopies
retro_chof_1909, retro_chof_2042, retro_chof_21,
Dasypus novemcinctus ENSDNOG000000067191 retrocopy
retro_dnov_32,
Echinops telfairi ENSETEG000000085261 retrocopy
retro_etel_41,
Macropus eugenii ENSMEUG000000108431 retrocopy
retro_meug_1374,
Myotis lucifugus ENSMLUG000000155093 retrocopies
retro_mluc_190, retro_mluc_427, retro_mluc_90,
Nomascus leucogenys ENSNLEG000000122331 retrocopy
retro_nleu_2313,
Oryctolagus cuniculus ENSOCUG000000040741 retrocopy
retro_ocun_38,
Oryctolagus cuniculus ENSOCUG000000058671 retrocopy
retro_ocun_720,
Oryctolagus cuniculus ENSOCUG00000008193 3 retrocopies
retro_ocun_1306, retro_ocun_1421 , retro_ocun_919,
Pongo abelii ENSPPYG000000024591 retrocopy
retro_pabe_3027,
Sorex araneus ENSSARG000000057781 retrocopy
retro_sara_732,
Tupaia belangeri ENSTBEG000000176163 retrocopies
retro_tbel_1555, retro_tbel_3014, retro_tbel_4616,
Tarsius syrichta ENSTSYG000000081555 retrocopies
retro_tsyr_1282, retro_tsyr_2102, retro_tsyr_858, retro_tsyr_9, retro_tsyr_92,
Vicugna pacos ENSVPAG000000106213 retrocopies
retro_vpac_12, retro_vpac_355, retro_vpac_651,


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