RetrogeneDB ID:

retro_cjac_51

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:69314662..69315100(+)
Located in intron of:ENSCJAG00000019368
Retrocopy
information
Ensembl ID:ENSCJAG00000035228
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000007532
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_51
ATGGGGAAAAAACAAAACAAGAAGACAGTGGAGGAGGTGCTAGAAGAGGAGGAAGAGGAATATGTGGTGGAAAAAGTTCT
CAACCTTCAAGTGGTAAAGGGCAAAGTGGAGTACCTCCTAAAGTGGAAGGGGTTCTCAGATGAGGACAATACATGGGAGC
CAGAAGAGAATATGGATTGCCCCAACCTCATTGCCGAGTTTCTGAAGTCACAGAAAACAGCACATGAGACAGATAAATCG
GAGGGAGGCAAGTGCAAAGCTGATTCTGATTCTGAAGATAAGGGAGAGGAGAGAAAACCAAAGAAGAAGAAAGAAGAGTC
AGAAAAGCCACGAGGCTTTGCTCAAGGTTTGAAGCCGGAGCGGATTATTGGAGCTACAGACTCTAGTGGAGAGCTCATGT
TCCTAATGAAATGGAAAAACTCTGATGAGGCTGACCTG

ORF - retro_cjac_51 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.0 %
Parental protein coverage: 79.37 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMGKKQNKKKVEEVLEEEEEEYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQS
MGKKQNKK.VEEVLEEEEEEYVVEKVL...VVKGKVEYLLKWKGFSDEDNTWEPEEN.DCP.LIAEFL.S
RetrocopyMGKKQNKKTVEEVLEEEEEEYVVEKVLNLQVVKGKVEYLLKWKGFSDEDNTWEPEENMDCPNLIAEFLKS
ParentalQKTAHETDKSEGGKRKADSDSEDKGEESKPKKKKEEVRLESEKPRGFARGLEPERIIGATDSSGELMFLM
QKTAHETDKSEGGK.KADSDSEDKGEE.KPKKKKEE....SEKPRGFA.GL.PERIIGATDSSGELMFLM
RetrocopyQKTAHETDKSEGGKCKADSDSEDKGEERKPKKKKEE----SEKPRGFAQGLKPERIIGATDSSGELMFLM
ParentalKWKNSDEADL
KWKNSDEADL
RetrocopyKWKNSDEADL

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 .29 RPM 29 .13 RPM
SRP051959_heart 0 .12 RPM 21 .71 RPM
SRP051959_kidney 2 .13 RPM 26 .29 RPM
SRP051959_liver 0 .48 RPM 12 .35 RPM
SRP051959_lung 0 .10 RPM 23 .02 RPM
SRP051959_lymph_node 0 .02 RPM 23 .52 RPM
SRP051959_skeletal_muscle 0 .00 RPM 20 .59 RPM
SRP051959_spleen 0 .02 RPM 25 .11 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_51 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_51 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_51 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 29 parental genes, and 120 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000048902 retrocopies
retro_amel_1228, retro_amel_54,
Bos taurus ENSBTAG000000029499 retrocopies
retro_btau_1121, retro_btau_1394, retro_btau_148, retro_btau_1583, retro_btau_1615, retro_btau_550, retro_btau_558, retro_btau_714, retro_btau_807,
Canis familiaris ENSCAFG000000168321 retrocopy
retro_cfam_804,
Choloepus hoffmanni ENSCHOG000000119572 retrocopies
retro_chof_1860, retro_chof_2185,
Callithrix jacchus ENSCJAG00000007532 2 retrocopies
retro_cjac_191, retro_cjac_51 ,
Callithrix jacchus ENSCJAG000000079528 retrocopies
retro_cjac_1100, retro_cjac_1414, retro_cjac_1612, retro_cjac_2405, retro_cjac_2623, retro_cjac_2728, retro_cjac_3322, retro_cjac_869,
Callithrix jacchus ENSCJAG000000188471 retrocopy
retro_cjac_2020,
Dipodomys ordii ENSDORG000000007162 retrocopies
retro_dord_594, retro_dord_709,
Erinaceus europaeus ENSEEUG000000048743 retrocopies
retro_eeur_121, retro_eeur_228, retro_eeur_396,
Echinops telfairi ENSETEG000000002037 retrocopies
retro_etel_1083, retro_etel_1572, retro_etel_1577, retro_etel_1611, retro_etel_2165, retro_etel_382, retro_etel_932,
Felis catus ENSFCAG000000060561 retrocopy
retro_fcat_514,
Homo sapiens ENSG000001084683 retrocopies
retro_hsap_4654, retro_hsap_4790, retro_hsap_4840,
Gorilla gorilla ENSGGOG000000240633 retrocopies
retro_ggor_2887, retro_ggor_3019, retro_ggor_330,
Microcebus murinus ENSMICG000000095104 retrocopies
retro_mmur_1324, retro_mmur_178, retro_mmur_467, retro_mmur_999,
Myotis lucifugus ENSMLUG000000050302 retrocopies
retro_mluc_1000, retro_mluc_1533,
Mustela putorius furoENSMPUG000000153021 retrocopy
retro_mputfur_1457,
Mus musculus ENSMUSG000000186661 retrocopy
retro_mmus_3108,
Nomascus leucogenys ENSNLEG000000024354 retrocopies
retro_nleu_1089, retro_nleu_1105, retro_nleu_1955, retro_nleu_2961,
Oryctolagus cuniculus ENSOCUG000000080213 retrocopies
retro_ocun_177, retro_ocun_442, retro_ocun_55,
Otolemur garnettii ENSOGAG000000056589 retrocopies
retro_ogar_1087, retro_ogar_1092, retro_ogar_1322, retro_ogar_2056, retro_ogar_2396, retro_ogar_2443, retro_ogar_2840, retro_ogar_2880, retro_ogar_368,
Ochotona princeps ENSOPRG000000036991 retrocopy
retro_opri_552,
Procavia capensis ENSPCAG000000023812 retrocopies
retro_pcap_134, retro_pcap_308,
Pongo abelii ENSPPYG000000088911 retrocopy
retro_pabe_78,
Rattus norvegicus ENSRNOG000000086892 retrocopies
retro_rnor_2388, retro_rnor_2841,
Sarcophilus harrisii ENSSHAG000000081921 retrocopy
retro_shar_76,
Sus scrofa ENSSSCG000000175291 retrocopy
retro_sscr_635,
Ictidomys tridecemlineatus ENSSTOG000000239863 retrocopies
retro_itri_1282, retro_itri_1599, retro_itri_1867,
Tupaia belangeri ENSTBEG0000001493139 retrocopies
retro_tbel_1388, retro_tbel_1557, retro_tbel_1613, retro_tbel_1655, retro_tbel_1663, retro_tbel_1794, retro_tbel_2124, retro_tbel_2130, retro_tbel_2281, retro_tbel_2313, retro_tbel_2346, retro_tbel_2539, retro_tbel_2559, retro_tbel_2571, retro_tbel_2587, retro_tbel_270, retro_tbel_2713, retro_tbel_2716, retro_tbel_2752, retro_tbel_2809, retro_tbel_2835, retro_tbel_2854, retro_tbel_2926, retro_tbel_2993, retro_tbel_303, retro_tbel_3236, retro_tbel_3370, retro_tbel_3685, retro_tbel_3998, retro_tbel_4032, retro_tbel_4202, retro_tbel_4611, retro_tbel_4630, retro_tbel_484, retro_tbel_558, retro_tbel_687, retro_tbel_792, retro_tbel_793, retro_tbel_938,
Tarsius syrichta ENSTSYG000000047692 retrocopies
retro_tsyr_1672, retro_tsyr_467,


Copyright © RetrogeneDB 2014-2017