RetrogeneDB ID:

retro_cjac_2214

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:21025516..21026152(-)
Located in intron of:ENSCJAG00000004780
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:YWHAB
Ensembl ID:ENSCJAG00000017664
Aliases:None
Description:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide [Source:HGNC Symbol;Acc:12849]


Retrocopy-Parental alignment summary:






>retro_cjac_2214
ATGACAATGGATAAAAGTGAGCTGGTATAGAAAGCCAAACTCTCTGAGCAGGCTGAGAGCTATGATGATATGGCTGCAGC
CACGAAGGCAGTCACAGAACAGGAGCATGAACTCTCCAATGAAGAGAGAAATCTGCTCTCTGTTGCCTACAAGAATGTGG
TAGGCACCCGCTGCTCTTCCCGGTGTGTCATCTCCAGCATTGAGCAGAAAACAGAGAGGAATGAGAAGCAGCAGCAGATG
GGCAAAGAATACTGTGAGAAGATAGAGGCAGAACTGCAGGACATCTGCAATGACGTTCTGGAGCTGTTGGACAAATATCT
GATTCCCAGTGCCACATAACCAGAAAGTAAGGCATTTTACCTGAAAATGAAAGATTATTTTAGGTATCTTTCTGAAGTGG
CATCTGGAGACAACCAACAAACCACTGTGTTGAACTCCCAGCAGGCTTACCAGGAAGCAATTAGAAATTAGAAAGAAATG
CAGCCTACACACCCAATTTGACTTGATCTGGCGCTTAATTTCTCAGTCTTTTACTATGACAATTCTCCTGAAAAGGCCTG
TGGCCTGGCAAAAATGGCATTTGGTGAACCAATTGCTAAATTGGATATACTGAATGAAGAGTCTTATTTGCACTCT

ORF - retro_cjac_2214 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.8 %
Parental protein coverage: 87.8 %
Number of stop codons detected: 4
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQK
MTMDKSELV.KAKL.EQAE.YDDMAAA.KAVTEQ.HELSNEERNLLSVAYKNVVG.R.SS..VISSIEQK
RetrocopyMTMDKSELV*KAKLSEQAESYDDMAAATKAVTEQEHELSNEERNLLSVAYKNVVGTRCSSRCVISSIEQK
ParentalTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNK
TERNEK.QQMGKEY.EKIEAELQDICNDVLELLDKYLIP.AT.PESK.FYLKMK.DYFRYLSEVASGDN.
RetrocopyTERNEKQQQMGKEYCEKIEAELQDICNDVLELLDKYLIPSAT*PESKAFYLKMK-DYFRYLSEVASGDNQ
ParentalQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNE
QTTV.NSQQAYQEA.....KEMQPTHPI.L.LALNFSVFYY...NSPEKAC.LAK.AF.E.IA.LD.LNE
RetrocopyQTTVLNSQQAYQEAIR-N*KEMQPTHPI*LDLALNFSVFYYD--NSPEKACGLAKMAFGEPIAKLDILNE
ParentalESYKDS
ESY..S
RetrocopyESYLHS

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 .27 RPM 142 .00 RPM
SRP051959_heart 0 .37 RPM 91 .24 RPM
SRP051959_kidney 0 .09 RPM 101 .57 RPM
SRP051959_liver 0 .02 RPM 65 .93 RPM
SRP051959_lung 0 .02 RPM 140 .83 RPM
SRP051959_lymph_node 0 .00 RPM 190 .27 RPM
SRP051959_skeletal_muscle 0 .52 RPM 55 .45 RPM
SRP051959_spleen 0 .08 RPM 184 .52 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_2214 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2214 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2214 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 27 parental genes, and 146 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000117961 retrocopy
retro_acar_8,
Choloepus hoffmanni ENSCHOG0000000578215 retrocopies
retro_chof_1049, retro_chof_1325, retro_chof_1630, retro_chof_1670, retro_chof_1975, retro_chof_22, retro_chof_2221, retro_chof_2350, retro_chof_2423, retro_chof_2619, retro_chof_326, retro_chof_352, retro_chof_487, retro_chof_707, retro_chof_971,
Callithrix jacchus ENSCJAG000000063942 retrocopies
retro_cjac_2197, retro_cjac_3127,
Callithrix jacchus ENSCJAG000000158445 retrocopies
retro_cjac_1769, retro_cjac_2164, retro_cjac_3000, retro_cjac_31, retro_cjac_881,
Callithrix jacchus ENSCJAG00000017664 2 retrocopies
retro_cjac_1002, retro_cjac_2214 ,
Dipodomys ordii ENSDORG0000000106414 retrocopies
retro_dord_235, retro_dord_236, retro_dord_255, retro_dord_256, retro_dord_258, retro_dord_259, retro_dord_262, retro_dord_263, retro_dord_332, retro_dord_442, retro_dord_545, retro_dord_681, retro_dord_725, retro_dord_9,
Echinops telfairi ENSETEG000000099674 retrocopies
retro_etel_1221, retro_etel_1380, retro_etel_1536, retro_etel_1705,
Homo sapiens ENSG000001669134 retrocopies
retro_hsap_4160, retro_hsap_4841, retro_hsap_622, retro_hsap_855,
Gorilla gorilla ENSGGOG000000045802 retrocopies
retro_ggor_2795, retro_ggor_699,
Microcebus murinus ENSMICG000000009737 retrocopies
retro_mmur_1044, retro_mmur_1100, retro_mmur_1288, retro_mmur_1576, retro_mmur_27, retro_mmur_305, retro_mmur_979,
Myotis lucifugus ENSMLUG000000063191 retrocopy
retro_mluc_871,
Macaca mulatta ENSMMUG000000132063 retrocopies
retro_mmul_1061, retro_mmul_236, retro_mmul_673,
Monodelphis domestica ENSMODG000000162002 retrocopies
retro_mdom_1557, retro_mdom_212,
Nomascus leucogenys ENSNLEG000000066432 retrocopies
retro_nleu_42, retro_nleu_422,
Oryctolagus cuniculus ENSOCUG000000030021 retrocopy
retro_ocun_273,
Otolemur garnettii ENSOGAG000000089093 retrocopies
retro_ogar_122, retro_ogar_1243, retro_ogar_2934,
Ochotona princeps ENSOPRG000000118362 retrocopies
retro_opri_56, retro_opri_924,
Pongo abelii ENSPPYG000000110415 retrocopies
retro_pabe_3453, retro_pabe_3454, retro_pabe_3519, retro_pabe_3520, retro_pabe_692,
Pan troglodytes ENSPTRG0000001352912 retrocopies
retro_ptro_1010, retro_ptro_1686, retro_ptro_2390, retro_ptro_2828, retro_ptro_2887, retro_ptro_3125, retro_ptro_3201, retro_ptro_3225, retro_ptro_412, retro_ptro_453, retro_ptro_594, retro_ptro_965,
Pteropus vampyrus ENSPVAG000000126621 retrocopy
retro_pvam_157,
Sarcophilus harrisii ENSSHAG000000112411 retrocopy
retro_shar_483,
Sus scrofa ENSSSCG000000073811 retrocopy
retro_sscr_506,
Ictidomys tridecemlineatus ENSSTOG000000037331 retrocopy
retro_itri_1214,
Tupaia belangeri ENSTBEG0000000280647 retrocopies
retro_tbel_1038, retro_tbel_1272, retro_tbel_1460, retro_tbel_1472, retro_tbel_1572, retro_tbel_1653, retro_tbel_1664, retro_tbel_2127, retro_tbel_2128, retro_tbel_2229, retro_tbel_2246, retro_tbel_228, retro_tbel_2371, retro_tbel_2373, retro_tbel_2379, retro_tbel_2397, retro_tbel_2512, retro_tbel_2536, retro_tbel_2540, retro_tbel_2542, retro_tbel_2583, retro_tbel_2584, retro_tbel_2615, retro_tbel_2617, retro_tbel_3502, retro_tbel_3554, retro_tbel_3604, retro_tbel_3642, retro_tbel_3743, retro_tbel_390, retro_tbel_3989, retro_tbel_3993, retro_tbel_40, retro_tbel_4101, retro_tbel_4121, retro_tbel_4338, retro_tbel_4447, retro_tbel_4456, retro_tbel_4459, retro_tbel_4510, retro_tbel_4514, retro_tbel_4604, retro_tbel_4664, retro_tbel_4690, retro_tbel_5, retro_tbel_705, retro_tbel_854,
Tarsius syrichta ENSTSYG000000065374 retrocopies
retro_tsyr_1065, retro_tsyr_1473, retro_tsyr_1637, retro_tsyr_2084,
Tursiops truncatus ENSTTRG000000076151 retrocopy
retro_ttru_762,
Vicugna pacos ENSVPAG000000050233 retrocopies
retro_vpac_396, retro_vpac_516, retro_vpac_9,


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