RetrogeneDB ID:

retro_cjac_480

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:164369508..164370800(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:AHCY
Ensembl ID:ENSCJAG00000018303
Aliases:None
Description:adenosylhomocysteinase [Source:HGNC Symbol;Acc:343]


Retrocopy-Parental alignment summary:






>retro_cjac_480
ATGTCTGACAAACTGCCCTACAAAGTTGGTGACATCAGCCTGGACACCTGGGAACACAAGACCCTGGATATTGCAGGGAA
TGAGTTGCCGGGCCTGGTGGCCATTCGGGAGCTGTACTTGCCCTCCAGGCCACTGAAGAGCACCCGCGTTGCTGGCTGCC
TGCAAATGAGTGTGGAGACGGCCATCCTCATTGAGACTCTCATCTCCCTGGGTGTTTGGGAGCAGTGGTCTAGTTGCAAC
ATCTTCTCCACCCAGGACCATGCAGCAGCTGCCTTTGCCAAGGCTGGCATGCCAGTGTTCACCCGGAAGGGCAAAATGAA
TGAGGAGTACCCTGGTGCATTGAACAGACACTGTACTTGAAGGATGGGCCCTTCAACGTGATTCTGGATGATGGGGGTGA
CCTTACTAACCTCATCCACACCAAGTACCCACAGCTCATGTCGAGCATCTGAGGCATCTCTTAGGATATCACAACCACGG
TCCACAACCTGTACAAGATGATGGCCAATGGAATCCTGAAGGTGCCTGCCATCAACATCAATGACTCCGTCACCAAGAGC
AAAATTTCACAACCTCTGTGGCTGCCAGGAGTCCCTCACAGATGAATGACATCAAGTGGGCCAAGACATAATGATTGCCA
GCCAGGTAGCAGTGGTAGCAGGCTAAGGCAATGTGGGTGGGGGCTGTGCCCACGCCCTGTGGGGTTTTGGGGCCCACGTC
ATCATCACCGAGACTGACCCTGTCAGTGTACTGCAGCTCCCATGGAAGGCTATGAGGTGACCACCACGGATGAGGCCTGT
CAAGAGGGCAACATCTTTGTCACCACCACAGCCTGTGTCGACATCATCCTTGGCCAGCACTTGCAGCAAATGAAAGATGA
TGTCATCGTGTGTAACACTGGATGCTTTGACGTGGAGATCAGTGTCAGGTAGCTCAACAAGAATGTTGCGGAGACGGTGA
ACATCAAGCCCCAGGTCGACCAGTACTGGCTGAAGAATGGGCGTCATATCATCCTGCTGGCTGAGGGTTGGCTGGTCAGC
CTGGGTTATGTCATGGGCTGCCCCAGCTTCATGGTGAGTAACACCTTCATCACCCAGGTGATGGTGCAGATTGAGCTGTG
AAGCCACTCAGACAAGTACCCCATCGGGGTTCACTTCCTGCCCAAGAAGCTGGATGACACAGTGGCTGAAGCTCCCCTGG
GCAAGCTGAATGTGAAATTGACCAAGCTGACTGAGAAGCAAGCCCGATAGCTGGGCATGTCCCGTGATGGCCCCTTCAAG
CCAGATCACTAC

ORF - retro_cjac_480 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.35 %
Parental protein coverage: 99.54 %
Number of stop codons detected: 7
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMSDKLPYKVADIGLADWGRKALNIAENEMPGLMRMRERYSTSKPLMGARIAGCLHMTVETAVLIETLVAL
MSDKLPYKV.DI.L..W..K.L.IA.NE.PGL...RE.Y..S.PL...R.AGCL.M.VETA.LIETL..L
RetrocopyMSDKLPYKVGDISLDTWEHKTLDIAGNELPGLVAIRELYLPSRPLKSTRVAGCLQMSVETAILIETLISL
ParentalGAEVRWSSCNIFSTQDHAAAAIAKAGIPVYAWKGETDEEYL-WCIEQTLYFKDGPLNMILDDGGDLTNLI
G....WSSCNIFSTQDHAAAA.AKAG.PV...KG...EEY..WCIEQTLY.KDGP.N.ILDDGGDLTNLI
RetrocopyGVWEQWSSCNIFSTQDHAAAAFAKAGMPVFTRKGKMNEEYP<WCIEQTLYLKDGPFNVILDDGGDLTNLI
ParentalHTKYPQLLPGIRGISEETTTGVHNLYKMMATGVLKVPAINVNDSVTKSK-FDNLYGCRESLIDGIKRA-T
HTKYPQL...I.GIS...TT.VHNLYKMMA.G.LKVPAIN.NDSVTKSK.F.NL.GC.ESL.D.......
RetrocopyHTKYPQLMSSI*GIS*DITTTVHNLYKMMANGILKVPAININDSVTKSK>FHNLCGCQESLTDE*HQVGQ
ParentalDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQ-AAMEGYEVTTMDEACQEGNIFVTTT
D.MIA..VAVVAG.G.VG.GCA.AL.GFGA.VIITE.DP...LQ.A.MEGYEVTT.DEACQEGNIFVTTT
RetrocopyDIMIASQVAVVAG*GNVGGGCAHALWGFGAHVIITETDPVSVLQ<APMEGYEVTTTDEACQEGNIFVTTT
ParentalGCVDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYRLKNGHRIILLAEGRLVN
.CVDIILG.H..QMKDD.IVCN.G.FDVEI.V..LN.N..E.VNIKPQVD.Y.LKNG..IILLAEG.LV.
RetrocopyACVDIILGQHLQQMKDDVIVCNTGCFDVEISVR*LNKNVAETVNIKPQVDQYWLKNGRHIILLAEGWLVS
ParentalLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQY
LG..MG.PSF..SN.F..QVM.QIEL..H.DKYP.GVHFLPKKLD..VAEA.LGKLNVKLTKLTEKQA..
RetrocopyLGYVMGCPSFMVSNTFITQVMVQIEL*SHSDKYPIGVHFLPKKLDDTVAEAPLGKLNVKLTKLTEKQAR*
ParentalLGMSRDGPFKPDHY
LGMSRDGPFKPDHY
RetrocopyLGMSRDGPFKPDHY

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
SRP051959_colon 0 .11 RPM 6 .66 RPM
SRP051959_heart 0 .23 RPM 7 .79 RPM
SRP051959_kidney 0 .00 RPM 49 .14 RPM
SRP051959_liver 0 .02 RPM 25 .54 RPM
SRP051959_lung 0 .03 RPM 4 .16 RPM
SRP051959_lymph_node 0 .00 RPM 3 .08 RPM
SRP051959_skeletal_muscle 0 .00 RPM 6 .38 RPM
SRP051959_spleen 0 .00 RPM 5 .86 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_480 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_480 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_480 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4213
Pan troglodytes retro_ptro_2860
Gorilla gorilla retro_ggor_2822
Pongo abelii retro_pabe_3446
Parental genes homology:
Parental genes homology involve 15 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000018303 7 retrocopies
retro_cjac_1028, retro_cjac_1248, retro_cjac_1806, retro_cjac_2132, retro_cjac_2839, retro_cjac_3287, retro_cjac_480 ,
Echinops telfairi ENSETEG000000025761 retrocopy
retro_etel_444,
Homo sapiens ENSG000001014446 retrocopies
retro_hsap_1496, retro_hsap_2325, retro_hsap_2365, retro_hsap_4213, retro_hsap_571, retro_hsap_803,
Gorilla gorilla ENSGGOG000000146945 retrocopies
retro_ggor_1148, retro_ggor_1795, retro_ggor_2822, retro_ggor_3087, retro_ggor_511,
Monodelphis domestica ENSMODG000000027531 retrocopy
retro_mdom_1974,
Mus musculus ENSMUSG000000275971 retrocopy
retro_mmus_197,
Nomascus leucogenys ENSNLEG000000100414 retrocopies
retro_nleu_1717, retro_nleu_2785, retro_nleu_40, retro_nleu_929,
Oryctolagus cuniculus ENSOCUG000000085921 retrocopy
retro_ocun_1886,
Pongo abelii ENSPPYG000000109359 retrocopies
retro_pabe_1247, retro_pabe_1978, retro_pabe_2108, retro_pabe_2189, retro_pabe_3446, retro_pabe_647, retro_pabe_658, retro_pabe_665, retro_pabe_718,
Pan troglodytes ENSPTRG000000134147 retrocopies
retro_ptro_1015, retro_ptro_1698, retro_ptro_1730, retro_ptro_2860, retro_ptro_3011, retro_ptro_559, retro_ptro_771,
Rattus norvegicus ENSRNOG000000177777 retrocopies
retro_rnor_1142, retro_rnor_1820, retro_rnor_1903, retro_rnor_2120, retro_rnor_569, retro_rnor_647, retro_rnor_839,
Sus scrofa ENSSSCG000000072781 retrocopy
retro_sscr_119,
Tarsius syrichta ENSTSYG000000071633 retrocopies
retro_tsyr_1178, retro_tsyr_1529, retro_tsyr_1582,
Tursiops truncatus ENSTTRG000000036321 retrocopy
retro_ttru_1666,
Xenopus tropicalis ENSXETG000000194861 retrocopy
retro_xtro_62,




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