RetrogeneDB ID:

retro_cjac_945

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:11:120742602..120743859(-)
Located in intron of:ENSCJAG00000002459
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000007491
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_945
ATGGCGTGTGCTTGCCCACTGATACCAGTGTACTCCGAAAAGGGGAGTCTCCTGGCAAAACTGTCACTTTGCCTGCTGTA
TTCAAGGCTCCTATTCGACCAGATATTGTGAACTTTGTTCACACCAACTTGCGCAAAAACAACAGACAGCCCTATGCAGC
CAGTGAATTAGCAGGCCATCAGACTAGTGCTGAGTCTTGGGGTACTGGCAGAGCTGCGGCTCGAATTCCCAGAGTTCGAG
GTGGTGGGACTCACCATTCTGGCCAGGGTGCTTTTGGAAATATGTGTTGCGGAGGCTGAATGTTTGCACCAACCAAAAGC
TGGCGCCGCTGGCATCGTAGAGTGAACACAACCCAAAAACGATATGCCATCTGTTCTGCCCTGGCTGCCTCAGCCTTACC
AGCACTGGTCATGTCTGAAGGTCATCGTATTGAGGAAGTTCCTGAACTTCCTTTGGTAGTCGAAGACAAAGTTGAAGGCT
ACAAGAAGACCAAGGAGGCTGTTTTGCTTCTCAAGAAACTTAAAGCCTGGAATGGTATCAAAACGGTCTATGCCTTTCAG
CGAATGAGAGCTGGCAAGGGCAAAATCGGAAACCGTGGCCCTATCCAGCGCCGAGGCCCCTGCACCATCTACGATGAACA
TAATGGTACCATCAGGGCCTTCAGAAACATCCCTGGAATTACTCTGCTTAATGTAAGCAAACTGAACATTCTGAAGCTTG
CTCCCAGTGGGCATGTGGGACGTTTCTGCATTTGGACCAAAAGTGCTTTTCTGAGTTAGATGAATTGTATGGCACTTGGT
GTAAAGCTGCTTCCCTCAAGAGTAACTACAATCTCCCCATGCACAAGATGATCAATACGGATCTCAGAAGAATCTTGAAA
AGCCCAGAGATCCAAAGAGCCCTTCGAGCACCACGCAAGAAGATTCAACGCAGAGTCCTAAATAAGAACCCATGAAAAAC
CTGAGAATCATGTTGAAGCTAAACCCATACGCAAAGACCACGCGCCGGAACACCATTCTCCGCCAGGCCAGGAATCACAA
GCTGCGGGTGGATAACGCGGCCGTGGCAGCAGCAGCACTAGAAGCCAAATCAGATGAGAAGGGGGTTGCAGGCAAGAAGG
AAAGGAAAGAAGGCTGCCGTTGGTGTTAAGAAGCAAAGAAGCCTCCGGTAGGAAAACAGGCAGCAGCTACCAAGAAACCA
GCCCTTGAAAAGAAGCCAGCAGAAAAGAAACCCACTACAGAGGAAAAGAAGCCTGCT

ORF - retro_cjac_945 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.51 %
Parental protein coverage: 99.77 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMACARPLISVYSEKG-ESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAESWGT
MACA.PLI.VYSEKG.ES.GK.VTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYA.SELAGHQTSAESWGT
RetrocopyMACACPLIPVYSEKG<ESPGKTVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAASELAGHQTSAESWGT
ParentalGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMS
GRA.ARIPRVRGGGTH.SGQGAFGNMC.GG.MFAPTK.WRRWHRRVNTTQKRYAICSALAASALPALVMS
RetrocopyGRAAARIPRVRGGGTHHSGQGAFGNMCCGG*MFAPTKSWRRWHRRVNTTQKRYAICSALAASALPALVMS
ParentalKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRRIQRRGPCI
.GHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWN.IK.VYA.QRMRAGKGK..NR..IQRRGPC.
RetrocopyEGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNGIKTVYAFQRMRAGKGKIGNRGPIQRRGPCT
ParentalIYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTESA-FRKLDELYGTWRKAASLKSNYN
IY.E.NG.I.AFRNIPGITLLNVSKLNILKLAP.GHVGRFCIWT.SA.F..LDELYGTW.KAASLKSNYN
RetrocopyIYDEHNGTIRAFRNIPGITLLNVSKLNILKLAPSGHVGRFCIWTKSA<FSELDELYGTWCKAASLKSNYN
ParentalLPMHKMINTDLSRILKSPEIQRALRAPRKKIHRRVLKKN-PLKNLRIMLKLNPYAKTMRRNTILRQARNH
LPMHKMINTDL.RILKSPEIQRALRAPRKKI.RRVL.KN.P.KNLRIMLKLNPYAKT.RRNTILRQARNH
RetrocopyLPMHKMINTDLRRILKSPEIQRALRAPRKKIQRRVLNKN<PMKNLRIMLKLNPYAKTTRRNTILRQARNH
ParentalKRRVDKAAAAAAAALEAKSDEKGVAGKKPVVVRKKGKKAAVGVKKQKKPPVGKKAAATKKPAPEKKPAEK
K.RVD..AA.AAAALEAKSDEKGVAGKK....RK.G.......KK...PPVGK.AAATKKPA.EKKPAEK
RetrocopyKLRVDN-AAVAAAALEAKSDEKGVAGKKE---RKEGCRWC*EAKK---PPVGKQAAATKKPALEKKPAEK
ParentalKPPTEEKKPA
KP.TEEKKPA
RetrocopyKPTTEEKKPA

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 1 .69 RPM 201 .42 RPM
SRP051959_heart 1 .32 RPM 222 .95 RPM
SRP051959_kidney 1 .60 RPM 238 .41 RPM
SRP051959_liver 0 .93 RPM 323 .78 RPM
SRP051959_lung 1 .79 RPM 319 .23 RPM
SRP051959_lymph_node 2 .65 RPM 428 .98 RPM
SRP051959_skeletal_muscle 0 .72 RPM 325 .67 RPM
SRP051959_spleen 1 .87 RPM 386 .75 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_945 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_945 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_945 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 31 parental genes, and 112 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000052112 retrocopies
retro_btau_101, retro_btau_610,
Canis familiaris ENSCAFG000000173091 retrocopy
retro_cfam_72,
Choloepus hoffmanni ENSCHOG000000030086 retrocopies
retro_chof_1014, retro_chof_1496, retro_chof_2219, retro_chof_2616, retro_chof_455, retro_chof_476,
Callithrix jacchus ENSCJAG00000007491 2 retrocopies
retro_cjac_251, retro_cjac_945 ,
Cavia porcellus ENSCPOG000000030551 retrocopy
retro_cpor_370,
Dasypus novemcinctus ENSDNOG000000066933 retrocopies
retro_dnov_1028, retro_dnov_1152, retro_dnov_1931,
Equus caballus ENSECAG000000231791 retrocopy
retro_ecab_428,
Echinops telfairi ENSETEG000000003373 retrocopies
retro_etel_1876, retro_etel_2195, retro_etel_226,
Felis catus ENSFCAG000000122934 retrocopies
retro_fcat_1136, retro_fcat_189, retro_fcat_505, retro_fcat_567,
Homo sapiens ENSG000001744445 retrocopies
retro_hsap_1306, retro_hsap_254, retro_hsap_2898, retro_hsap_4229, retro_hsap_471,
Gorilla gorilla ENSGGOG000000036954 retrocopies
retro_ggor_1023, retro_ggor_2008, retro_ggor_2831, retro_ggor_304,
Loxodonta africana ENSLAFG000000064943 retrocopies
retro_lafr_1076, retro_lafr_152, retro_lafr_960,
Microcebus murinus ENSMICG000000044196 retrocopies
retro_mmur_1050, retro_mmur_1330, retro_mmur_440, retro_mmur_562, retro_mmur_830, retro_mmur_852,
Myotis lucifugus ENSMLUG000000118092 retrocopies
retro_mluc_121, retro_mluc_198,
Macaca mulatta ENSMMUG000000168442 retrocopies
retro_mmul_2160, retro_mmul_649,
Monodelphis domestica ENSMODG000000096572 retrocopies
retro_mdom_656, retro_mdom_944,
Mustela putorius furoENSMPUG000000003373 retrocopies
retro_mputfur_1205, retro_mputfur_411, retro_mputfur_570,
Mus musculus ENSMUSG000000323992 retrocopies
retro_mmus_2863, retro_mmus_495,
Nomascus leucogenys ENSNLEG000000129384 retrocopies
retro_nleu_1041, retro_nleu_1062, retro_nleu_2385, retro_nleu_887,
Oryctolagus cuniculus ENSOCUG000000087943 retrocopies
retro_ocun_1134, retro_ocun_630, retro_ocun_631,
Ochotona princeps ENSOPRG000000077921 retrocopy
retro_opri_735,
Pongo abelii ENSPPYG000000065781 retrocopy
retro_pabe_152,
Pan troglodytes ENSPTRG000000071956 retrocopies
retro_ptro_1512, retro_ptro_1959, retro_ptro_214, retro_ptro_2873, retro_ptro_353, retro_ptro_897,
Pteropus vampyrus ENSPVAG0000000006818 retrocopies
retro_pvam_1222, retro_pvam_1342, retro_pvam_201, retro_pvam_202, retro_pvam_216, retro_pvam_236, retro_pvam_267, retro_pvam_399, retro_pvam_428, retro_pvam_430, retro_pvam_435, retro_pvam_466, retro_pvam_518, retro_pvam_736, retro_pvam_778, retro_pvam_819, retro_pvam_865, retro_pvam_955,
Rattus norvegicus ENSRNOG000000093785 retrocopies
retro_rnor_1192, retro_rnor_1621, retro_rnor_2061, retro_rnor_2484, retro_rnor_949,
Sus scrofa ENSSSCG000000049452 retrocopies
retro_sscr_138, retro_sscr_885,
Ictidomys tridecemlineatus ENSSTOG000000092211 retrocopy
retro_itri_437,
Tupaia belangeri ENSTBEG000000143929 retrocopies
retro_tbel_1701, retro_tbel_2186, retro_tbel_2649, retro_tbel_3302, retro_tbel_3577, retro_tbel_3624, retro_tbel_3938, retro_tbel_4340, retro_tbel_4402,
Tarsius syrichta ENSTSYG000000055881 retrocopy
retro_tsyr_1144,
Tursiops truncatus ENSTTRG000000102067 retrocopies
retro_ttru_1130, retro_ttru_1399, retro_ttru_1713, retro_ttru_177, retro_ttru_789, retro_ttru_817, retro_ttru_964,
Vicugna pacos ENSVPAG000000067462 retrocopies
retro_vpac_143, retro_vpac_250,


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