RetrogeneDB ID:

retro_sscr_9

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:1:267166210..267167764(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSSCG00000005361
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:ALDH2
Ensembl ID:ENSSSCG00000009889
Aliases:None
Description:Sus scrofa aldehyde dehydrogenase 2 family (mitochondrial) (ALDH2), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001044611]


Retrocopy-Parental alignment summary:






>retro_sscr_9
ATGCTGCACTTCCTGGTGCCCCGGCTGTTTGGCCTGTGCCGCCCCGTTGCCCCGTACTCCTCTGCAGCAGCCCTCCCAAG
CCCCATCCTCAATCCGGACATCCGCTACAACCAGCTCTTCATCAACAATGAGTGGCAAGATGCGGTCAGCAAGAAGACCT
TCCAGACAGTCAACCCCACCACAGGGGAGGTCATTGGCCACGTGGCTGAAGGGGACCAGGCTGATGTGGATCGGGCAGTG
AAAGCAGCCCGTGAGGCCTTCCGCCTGGGGTCTCCATGGCGCCGGATGGATGCCTCAGAGCGGGGCCGGCTGCTGAACCG
CCTGGCTGATCTAGTGGAGCGGGATCGTGTCTACTTGGCCTCGCTGGAAACCCTGGACAACGGCAAGCCTTTCCAGGAGT
CTTACGCCTTGGACCTGGATGAGGTCATCAAGGTGTACCGGTACTTTGCTGGCTGGGCTGACAAGTGGCATGGCAAGACC
ATCCCCATGGATGGTGAGCATTTCTGCTTTACCCGGCATGAGCCCGTTGGCGTCTGTGGCCAGATAATCCCATGGAACTT
TCCCTTGGTCATGCAGGCCTGGAAGCTCGCCCCGGCCCTTGCCACAGGCAATACTGTGGTCATGAAGGTGGCAGAGCAGA
CCCCCCTTTCTGCTCTGTACTTGGCCTCCCTCATCAAAGAGGTGGGCTTTCCCCCTGGGGTGGTGAACATCCTCACAGGC
TATGGCCCAACAGCAGGAACAGCTATCGCCCATCACATGGATGTCAACAAAGTTGCCTTCACTGGCTCTACCGAGGTGGG
CCACCTGATCCAGAAGGCGGCTGGTGATTCCAACCTCAAGAGAGTCACCCTGGAGCTGGGTGGGAAGAGTCCGAGCATCG
TGTTGGCTGATGCCGACATGGACCACGCTGTGGAGCAGTGCCATGAAGCCCTGTTCTTCAACATGGGCCAGTGCTGCTGT
GCAGGTTCCCGGACCTTCGTTGAGGAATCCATCTATGATGAGTTTCTCGAGAGAACCGTGGAGAAAGCTAAGCGGCGGAA
AGTTGGGAACCCCTTTGAGCTAGACACCCAGCAGGGGCCCCAGGTGAACAAGGAGCAGTTTGAGCGAATCCTGGGCTACA
TCCAGCTTGGCCAGAAGGAAGGGGCAAAACTTCTCTGTGGCGGGGAGCGTTTTGGAGAGCGAGGCTTCTTCATCAAGCCC
ACGGTCTTTGGTGGAGTGCAAGATGACATGAGGATCGCCAAGGAGGAGATCTTTGGGCCTGTGCAGCCTCTGTTCAAGTT
CAAGAGGATCGAGGAGGTGATCGAGAGGGCCAACAACACTAGGTATGGCTTGGCGGCTGCCGTGTTCACTCAGGACCTGG
ACAAAGCCATGTACTTCACACAGGCCCTCCAAGCTGGGACAGTGTGGGTGAACACCTACAACATTGTCACCTGCCACACA
CCTTTCGGAGGCTTTAAGGAATCTGGCAATGGAAGGGAGCTGGGGGAGGATGGGCTTAAGGCCTACACAGAGGTGAAGAC
AGTCACCATCAAGGTTCCTCAGAAGGACTCCTAA

ORF - retro_sscr_9 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.49 %
Parental protein coverage: 94.82 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalAVPAPNQQPEIFYNQIFINNEWHDAISKKTFPTVNPSTGDVICHVAEGDKEDVDRAVEAARAAFQLGSPW
A.P.P...P.I.YNQ.FINNEW.DA.SKKTF.TVNP.TG.VI.HVAEGD..DVDRAV.AAR.AF.LGSPW
RetrocopyALPSPILNPDIRYNQLFINNEWQDAVSKKTFQTVNPTTGEVIGHVAEGDQADVDRAVKAAREAFRLGSPW
ParentalRRLDASDRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTLPI
RR.DAS.RGRLLNRLADL.ERDR.YLA.LETLDNGKP...SY..DLD.V.K..RY.AGWADK.HGKT.P.
RetrocopyRRMDASERGRLLNRLADLVERDRVYLASLETLDNGKPFQESYALDLDEVIKVYRYFAGWADKWHGKTIPM
ParentalDGDYFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVSEQTPLTALYVANLIKEAGFPPG
DG..F..TRHEPVGVCGQIIPWNFPL.MQAWKL.PALATGN.VVMKV.EQTPL.ALY.A.LIKE.GFPPG
RetrocopyDGEHFCFTRHEPVGVCGQIIPWNFPLVMQAWKLAPALATGNTVVMKVAEQTPLSALYLASLIKEVGFPPG
ParentalVVNIVPGYGPTAGAAIASHEDVDKVAFTGSTEVGHLIQVAAGKSNLKRVTLELGGKSPNIIMSDADMDWA
VVNI..GYGPTAG.AIA.H.DV.KVAFTGSTEVGHLIQ.AAG.SNLKRVTLELGGKSP.I...DADMD.A
RetrocopyVVNILTGYGPTAGTAIAHHMDVNKVAFTGSTEVGHLIQKAAGDSNLKRVTLELGGKSPSIVLADADMDHA
ParentalVEQAHFALFFNQGQCCCAGSRTFVQEDIYAEFVERSVARARSRVVGNPFDSRTEQGPQIDETQFKKILGY
VEQ.H.ALFFN.GQCCCAGSRTFV.E.IY.EF.ER.V..A..R.VGNPF...T.QGPQ....QF..ILGY
RetrocopyVEQCHEALFFNMGQCCCAGSRTFVEESIYDEFLERTVEKAKRRKVGNPFELDTQQGPQVNKEQFERILGY
ParentalIKSGKEEGAKLLCGGGAAADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVIGRANNSKYG
I..G..EGAKLLCGG.....RG.FI.PTVFG.VQD.M.IAKEEIFGPV....KFK.IEEVI.RANN..YG
RetrocopyIQLGQKEGAKLLCGGERFGERGFFIKPTVFGGVQDDMRIAKEEIFGPVQPLFKFKRIEEVIERANNTRYG
ParentalLAAAVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKLSGSGRELGEYGLQAYTEVKTVTVKVP
LAAAVFT.DLDKA.Y..QALQAGTVWVN.Y.......PFGG.K.SG.GRELGE.GL.AYTEVKTVT.KVP
RetrocopyLAAAVFTQDLDKAMYFTQALQAGTVWVNTYNIVTCHTPFGGFKESGNGRELGEDGLKAYTEVKTVTIKVP
ParentalQKNS
QK.S
RetrocopyQKDS

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
SRP014902_placenta 4 .51 RPM 152 .11 RPM
SRP014902_testis 14 .43 RPM 46 .25 RPM
SRP018288_heart 1 .81 RPM 4 .51 RPM
SRP018288_kidney 192 .97 RPM 556 .06 RPM
SRP018288_liver 13 .11 RPM 1003 .91 RPM
SRP018288_lung 5 .40 RPM 95 .00 RPM
SRP018856_adipose 19 .63 RPM 160 .93 RPM
SRP035408_brain 5 .37 RPM 44 .24 RPM
SRP035408_liver 30 .71 RPM 422 .87 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

2 EST(s) were mapped to retro_sscr_9 retrocopy
EST ID Start End Identity Match Mis-match Score
EW063269 267166624 267167187 99.5 560 3 557
FS675436 267166197 267167036 100 839 0 839

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_9 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_9 has 8 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_19
Pan troglodytes retro_ptro_118
Gorilla gorilla retro_ggor_33
Pongo abelii retro_pabe_32
Macaca mulatta retro_mmul_247
Mus musculus retro_mmus_222
Rattus norvegicus retro_rnor_307
Bos taurus retro_btau_48
Parental genes homology:
Parental genes homology involve 21 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000136641 retrocopy
retro_amel_51,
Bos taurus ENSBTAG000000087431 retrocopy
retro_btau_48,
Canis familiaris ENSCAFG000000086831 retrocopy
retro_cfam_1493,
Equus caballus ENSECAG000000176732 retrocopies
retro_ecab_1054, retro_ecab_1061,
Felis catus ENSFCAG000000220001 retrocopy
retro_fcat_1590,
Homo sapiens ENSG000001112751 retrocopy
retro_hsap_19,
Gorilla gorilla ENSGGOG000000071081 retrocopy
retro_ggor_33,
Latimeria chalumnae ENSLACG000000117981 retrocopy
retro_lcha_108,
Microcebus murinus ENSMICG000000034871 retrocopy
retro_mmur_19,
Myotis lucifugus ENSMLUG000000170841 retrocopy
retro_mluc_1918,
Macaca mulatta ENSMMUG000000083361 retrocopy
retro_mmul_247,
Mustela putorius furoENSMPUG000000022821 retrocopy
retro_mputfur_27,
Mus musculus ENSMUSG000000294551 retrocopy
retro_mmus_222,
Nomascus leucogenys ENSNLEG000000000161 retrocopy
retro_nleu_22,
Otolemur garnettii ENSOGAG000000330931 retrocopy
retro_ogar_203,
Pongo abelii ENSPPYG000000049661 retrocopy
retro_pabe_32,
Pteropus vampyrus ENSPVAG000000131891 retrocopy
retro_pvam_163,
Rattus norvegicus ENSRNOG000000013441 retrocopy
retro_rnor_307,
Sus scrofa ENSSSCG00000009889 1 retrocopy
retro_sscr_9 ,
Ictidomys tridecemlineatus ENSSTOG000000150091 retrocopy
retro_itri_33,
Xenopus tropicalis ENSXETG000000209301 retrocopy
retro_xtro_12,


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