RetrogeneDB ID:

retro_cjac_1806

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:65669581..65670331(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000033820
Aliases:None
Status:KNOWN_PSEUDOGENE
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_1806
ACTGTCACCCAGAGCAAGTTTGACAACCTCTATGGCTGTCGGGAGTCCCTCATAGATGGTATCAAGCGAGCCACTGATGT
GATGATTGCCGTCAAGGTAGCAGTGGTAGCAGGTTATGGCGATGTGGGCAAGGGCTGTGCCCAGGCCCTGCGGGGTTTCA
GGGCCCACGTCATCATCACCAAGACTGACCCCATCAAGGCACTGCAGGCCGCCATGGAGGGCTATGAGGTGACCACCATG
GATGAGGCCTGTCAGGAGGGCAATATCTTCGTCACTACCACAGGCTGTGTTGACATCATCCTTGGCCACCACTTTGAGCA
AATGAAGGATGATGCCATCGTGTGTAACATTGGACACTTTGATGTGGAGGTCAATGTCAAGTGGCTCAACGGGAATGTTG
TGGAGAAGGTGAACATCAAGCCGCAGGTGGAACAGTACTGGCTGAAGAATGGGCGCCACATCATCCTGCTGGCAGAGGGT
CGGCTGGTCAATCTGGGTTGTGCCATGGGCCACCCCAGCTTCGTGATGAGTAACTCCTTCACCAACCAGGTGATGGCTCA
GATCGAGCTGTGGACTCACCCTGACAAGTACCCTGTTGGGGTTCACTTCCTGCCCAAGAAGCTGGATGAGGCAGTGATTG
AAGCCCACCTGGGCAAGCTGAACATGAAGTTGACCAAGCTGAAAGAGAAGCAGGCTCAGTACCTGGGCATGTCCCGTAAT
GGCCCCTTCAAGTTGGATCACTACCGCTAC

ORF - retro_cjac_1806 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.8 %
Parental protein coverage: 61.88 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQA
.VT.SKFDNLYGCRESLIDGIKRATDVMIA.KVAVVAGYGDVGKGCAQALRGF.A.VIIT..DPI.ALQA
RetrocopyTVTQSKFDNLYGCRESLIDGIKRATDVMIAVKVAVVAGYGDVGKGCAQALRGFRAHVIITKTDPIKALQA
ParentalAMEGYEVTTMDEACQEGNIFVTTTGCVDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIK
AMEGYEVTTMDEACQEGNIFVTTTGCVDIILG.HFEQMKDDAIVCNIGHFDVE..VKWLN.N.VEKVNIK
RetrocopyAMEGYEVTTMDEACQEGNIFVTTTGCVDIILGHHFEQMKDDAIVCNIGHFDVEVNVKWLNGNVVEKVNIK
ParentalPQVDRYRLKNGHRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDE
PQV..Y.LKNG..IILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDE
RetrocopyPQVEQYWLKNGRHIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDE
ParentalAVAEAHLGKLNVKLTKLTEKQAQYLGMSRDGPFKPDHYRY
AV.EAHLGKLN.KLTKL.EKQAQYLGMSR.GPFK.DHYRY
RetrocopyAVIEAHLGKLNMKLTKLKEKQAQYLGMSRNGPFKLDHYRY

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 .00 RPM 6 .66 RPM
SRP051959_heart 0 .00 RPM 7 .79 RPM
SRP051959_kidney 0 .00 RPM 49 .14 RPM
SRP051959_liver 0 .00 RPM 25 .54 RPM
SRP051959_lung 0 .00 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_1806 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1806 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1806 has 0 orthologous retrocopies within eutheria group .

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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