RetrogeneDB ID:

retro_rnor_1967

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:4:48331354..48332765(+)
Located in intron of:ENSRNOG00000029610
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Sdad1
Ensembl ID:ENSRNOG00000022229
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_rnor_1967
TTTCTCCAGCAATATAATCATGATAAATCCAATATGGAGATTTTCAAGTTACAACCAAATAGACCCAGCAAAGAACATTC
AGAACTGGTGATATTCATGGCACAGATTGGCCACTGCTACCCGAAGCATCTCAGTAACTCCCCGCAGGAGCTGAAGGACC
TGCTCTCCTACAACCACACCGTCTTAGACCCAGACCTCCACATGACATTTTGCAGAGCCTTGATCTTACTGAGAACTAAG
AATCTCATCAACCCATCACGTTTGCTAGAGCTCTTCTTTGAGCTTCGGCGCTGCCACAACAAGGTCCTGCAGAGGACTCT
ATACACACATATCGTGACTGACATCAAGAACATCAACGCCAAAGACAAGAAGAACAAGTTGAACTTGGGGCTGCAGAACT
TCATGTACTCCACGTTGAGAGACAGCAACGCAACCACAGCCAAGATGTCTCTGGATGTGACGATTGAACTCTACAGAAAC
ATCTGGAATGATGCCAAAACTGTCAATGTTATCACAACTTCATGTCTCTCAAAGATCGCCAAGATATTAGTTGCTGCTTT
GACCTTCTTCCTCGGGAAAGATGAGGAAGAGAGGCAGAACAGCGGACTCCGAATCTGAGGCTGACGGAACCACAGCGAGA
GACCTGCTGGTGGAGTGTGCCACGGAAAAGGAGGGCTCCAAAAACAAGGAGCTGGAAACGGTGATGGAAGTGTGGAAGAA
ACTTAAGAAGAAGAAACCAGAAGTGTGTCGACTTTTCAGCTACTCACTTGTCTCATGATCCCCGAGACTTTGCAGAAAAG
CTTCCGAAGCAGCTGGAGAGCTGGGAGGAGACGTTTGACGTGAAGATGATGCTCACGAGCCTCGTCTCCAGATTGGTGGG
GATTCACAAGCTTTTCCTCTTCAACTTCTACCCTTTCATGCAAAGGTTTCTGCACCCCCACCAGCGAGAGAAGTCACGAA
GATCCTTCTGTTCGCTGCAGGTGCCTCTCCTCACCTGCTGCCTCCAGAGGTTATTCAGTCTTTGCTCGTGATGGTGGCCA
ACAGTTTTGCTACTGACAAGAATTCTGGGAAAGTCGTGACCGTAAGAATCAATGCTAGAAAAGAGATCACAGCTTGATGT
CCTTTGGCCATGTCTAAAGAACTTCTTCAGGACCTGGCTCAATATAAGACACACAAAGATAAGAAGGTAGTGATGTCTGC
CATAAGTTTGATCCATCTGTTATGGACCCTGAACCCTCAAATGTTGCGGAAGTTACGGGGTAAACCCACTAAAGCCTCCA
TCCTAGCAAGAATACAAGAGTATGGAGTATTAGATGCTAAAGATTACATCCCGAGAGCAGAGCTTCTAGAGCTTGAGGAA
GAAGAGAATTCAGAAAATGATGAAGATGTGTGGGAAAGTGCCAGGCTCAGT

ORF - retro_rnor_1967 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.26 %
Parental protein coverage: 68.95 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalFLQQYNHYKSNMEIFKLQPNKPSKELAELVMFMAQIGHCYPEHLSEFPQELKDLLSYNHTVLDPDLRMTF
FLQQYNH.KSNMEIFKLQPN.PSKE..ELV.FMAQIGHCYP.HLS..PQELKDLLSYNHTVLDPDL.MTF
RetrocopyFLQQYNHDKSNMEIFKLQPNRPSKEHSELVIFMAQIGHCYPKHLSNSPQELKDLLSYNHTVLDPDLHMTF
ParentalCKALILLRNKNLINPSDLLELFFELLRCRDKLLRKTLYTHIVTDIKNINAKHKNNKVNVVLQNFMYTMLR
C.ALILLR.KNLINPS.LLELFFEL.RC..K.L..TLYTHIVTDIKNINAK.K.NK.N..LQNFMY..LR
RetrocopyCRALILLRTKNLINPSRLLELFFELRRCHNKVLQRTLYTHIVTDIKNINAKDKKNKLNLGLQNFMYSTLR
ParentalDSNATAAKMSLDVMIELYRRNIWNDAKTVNVITTACFSKITKILVAALTFFLGKDEEEKQDS-DSESEDD
DSNAT.AKMSLDV.IELY.RNIWNDAKTVNVITT.C.SKI.KILVAALTFFLGKDEEE.Q.S.DSESE.D
RetrocopyDSNATTAKMSLDVTIELY-RNIWNDAKTVNVITTSCLSKIAKILVAALTFFLGKDEEERQNS>DSESEAD
ParentalGPTARDLLVQYATGKKGSKNKKKLEKAMKVLKKQKKKKKPEV-FNFSAIHLIHDPQDFAEKLLKQLESCK
G.TARDLLV..AT.K.GSKN.K.LE..M.V.KK..KKKKPEV...FSA.HL.HDP.DFAEKL.KQLES..
RetrocopyGTTARDLLVECATEKEGSKN-KELETVMEVWKK-LKKKKPEV>VDFSATHLSHDPRDFAEKLPKQLESWE
ParentalERFEVKMMLMNLISRLVGIHELFLFNFYPFVQRFLQPHQREVTK-ILLFAAQASHHLVPPEIIQSLLLTV
E.F.VKMML..L.SRLVGIH.LFLFNFYPF.QRFL.PHQRE......L..A........P......LL..
RetrocopyETFDVKMMLTSLVSRLVGIHKLFLFNFYPFMQRFLHPHQREKSR<KILLFAAGASPHLLPPEVIQSLLVM
ParentalANN-FVTDKNSGEVMTVGINAIKEITARCPLAMTEELLQDLAQYKTHKDKNVMMSARTLIHLFRTLNPQM
..N.F.TDKNSG.V.TV.INA.KEITA.CPLAM..ELLQDLAQYKTHKDK.V.MSA..LIHL..TLNPQM
RetrocopyVANSFATDKNSGKVVTVRINARKEITA*CPLAMSKELLQDLAQYKTHKDKKVVMSAISLIHLLWTLNPQM
ParentalLQKKFRGKPTEASIEARIQEYGELDAKDYIPGAEVLELEKEENTENDEDGWESASLS
L..K.RGKPT.ASI.ARIQEYG.LDAKDYIP.AE.LELE.EEN.ENDED.WESA.LS
RetrocopyL-RKLRGKPTKASILARIQEYGVLDAKDYIPRAELLELEEEENSENDEDVWESARLS

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 0 .07 RPM 10 .64 RPM
SRP017611_kidney 0 .00 RPM 11 .51 RPM
SRP017611_liver 0 .00 RPM 5 .11 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_1967 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1967 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1967 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000085212 retrocopies
retro_cfam_1211, retro_cfam_515,
Cavia porcellus ENSCPOG000000085242 retrocopies
retro_cpor_510, retro_cpor_994,
Echinops telfairi ENSETEG000000048112 retrocopies
retro_etel_1946, retro_etel_779,
Homo sapiens ENSG000001983012 retrocopies
retro_hsap_2412, retro_hsap_4030,
Gorilla gorilla ENSGGOG000000064411 retrocopy
retro_ggor_1498,
Loxodonta africana ENSLAFG000000122171 retrocopy
retro_lafr_980,
Microcebus murinus ENSMICG000000066821 retrocopy
retro_mmur_1204,
Macaca mulatta ENSMMUG000000175031 retrocopy
retro_mmul_604,
Nomascus leucogenys ENSNLEG000000270341 retrocopy
retro_nleu_2410,
Oryctolagus cuniculus ENSOCUG000000269531 retrocopy
retro_ocun_547,
Pongo abelii ENSPPYG000000148521 retrocopy
retro_pabe_1777,
Pan troglodytes ENSPTRG000000243992 retrocopies
retro_ptro_1388, retro_ptro_2732,
Rattus norvegicus ENSRNOG00000022229 2 retrocopies
retro_rnor_1381, retro_rnor_1967 ,
Sus scrofa ENSSSCG000000089741 retrocopy
retro_sscr_571,
Tupaia belangeri ENSTBEG000000052701 retrocopy
retro_tbel_2414,


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