RetrogeneDB ID:

retro_mmul_59

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:1:133906195..133906672(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMMUG00000008823
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.2587
Ensembl ID:ENSMMUG00000003636
Aliases:None
Description:transcription factor BTF3 homolog 4 [Source:RefSeq peptide;Acc:NP_001253910]


Retrocopy-Parental alignment summary:






>retro_mmul_59
ATGAATCAAGAAAAGTTAGCCAAACTTCAGGCTCAGGTCCGGATAGGGGGCAAGGGTACAGCTCGCAGAAAGAAGAAGGT
GGTATACAGAACAGCTACAGCTGATGACAAAAAGCTTCAGAGTTCTCTAAAAAAACTGGCTGTGAATAATATAGCTGGTA
TTGAAGAGGTGAACATGATTAAAGATGATGGGACAGTTATTCATTTCAACAATCCCAAAGTCCAAGCTTCCCTTTCTGCT
AACACCTTTGCAATTACTGGTCATGCAGAAGCCAAACCAATCACAGAAATGTTTCCTGGAATATTAAGTCAGCTTGGTGC
TGACAGTTTAACAAGCCTTAGGAAGTTAGCTGAACAGTTCCCACGGCAAGTCTTGGACAGTAAAGCACCAAAACCAGAAG
ACATTGATGAGGAGGATGATGATGTTCCAGATCTTGTAGAAAATTTTGATGAGGCATCAAAGAATGAAGCTAACTAA

ORF - retro_mmul_59 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.87 %
Parental protein coverage: 92.76 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalQGTARRKKKVVHRTATADDKKLQSSLKKLAVNNIAGIEEVNMIKDDGTVIHFNNPKVQASLSANTFAITG
.GTARRKKKVV.RTATADDKKLQSSLKKLAVNNIAGIEEVNMIKDDGTVIHFNNPKVQASLSANTFAITG
RetrocopyKGTARRKKKVVYRTATADDKKLQSSLKKLAVNNIAGIEEVNMIKDDGTVIHFNNPKVQASLSANTFAITG
ParentalHAEAKPITEMLPGILSQLGADSLTSLRKLAEQFPRQVLDSKAPKPEDIDEEDDDVPDLVENFDEASKNEA
HAEAKPITEM.PGILSQLGADSLTSLRKLAEQFPRQVLDSKAPKPEDIDEEDDDVPDLVENFDEASKNEA
RetrocopyHAEAKPITEMFPGILSQLGADSLTSLRKLAEQFPRQVLDSKAPKPEDIDEEDDDVPDLVENFDEASKNEA
ParentalN
N
RetrocopyN

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
SRP007412_brain 1 .68 RPM 29 .47 RPM
SRP007412_brain_prefrontal_cortex 2 .94 RPM 23 .88 RPM
SRP007412_cerebellum 0 .97 RPM 24 .73 RPM
SRP007412_heart 1 .59 RPM 11 .72 RPM
SRP007412_kidney 1 .29 RPM 8 .69 RPM
SRP007412_liver 1 .27 RPM 7 .92 RPM
SRP007412_testis 2 .11 RPM 13 .08 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_59 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_59 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_59 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 30 parental genes, and 120 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000110251 retrocopy
retro_btau_1030,
Canis familiaris ENSCAFG000000037822 retrocopies
retro_cfam_2135, retro_cfam_938,
Callithrix jacchus ENSCJAG000000215824 retrocopies
retro_cjac_2000, retro_cjac_2929, retro_cjac_4160, retro_cjac_451,
Cavia porcellus ENSCPOG000000040061 retrocopy
retro_cpor_908,
Ciona savignyi ENSCSAVG000000096531 retrocopy
retro_csav_25,
Dasypus novemcinctus ENSDNOG000000031814 retrocopies
retro_dnov_1690, retro_dnov_1928, retro_dnov_2672, retro_dnov_921,
Erinaceus europaeus ENSEEUG000000045023 retrocopies
retro_eeur_215, retro_eeur_447, retro_eeur_456,
Echinops telfairi ENSETEG0000001192311 retrocopies
retro_etel_1017, retro_etel_1167, retro_etel_1207, retro_etel_1409, retro_etel_1990, retro_etel_2113, retro_etel_2203, retro_etel_291, retro_etel_663, retro_etel_804, retro_etel_953,
Homo sapiens ENSG000001347173 retrocopies
retro_hsap_2173, retro_hsap_2514, retro_hsap_3669,
Loxodonta africana ENSLAFG000000161243 retrocopies
retro_lafr_206, retro_lafr_769, retro_lafr_947,
Macropus eugenii ENSMEUG0000000613510 retrocopies
retro_meug_1114, retro_meug_1164, retro_meug_1333, retro_meug_1395, retro_meug_1512, retro_meug_1663, retro_meug_2008, retro_meug_298, retro_meug_903, retro_meug_966,
Microcebus murinus ENSMICG000000028071 retrocopy
retro_mmur_804,
Myotis lucifugus ENSMLUG000000168841 retrocopy
retro_mluc_912,
Macaca mulatta ENSMMUG00000003636 1 retrocopy
retro_mmul_59 ,
Macaca mulatta ENSMMUG000000222912 retrocopies
retro_mmul_105, retro_mmul_2424,
Monodelphis domestica ENSMODG000000007702 retrocopies
retro_mdom_33, retro_mdom_992,
Mustela putorius furoENSMPUG000000069662 retrocopies
retro_mputfur_1444, retro_mputfur_924,
Mus musculus ENSMUSG000000285682 retrocopies
retro_mmus_1134, retro_mmus_2743,
Nomascus leucogenys ENSNLEG000000160412 retrocopies
retro_nleu_1439, retro_nleu_521,
Oryctolagus cuniculus ENSOCUG000000015173 retrocopies
retro_ocun_1001, retro_ocun_1412, retro_ocun_1912,
Otolemur garnettii ENSOGAG000000302562 retrocopies
retro_ogar_2759, retro_ogar_570,
Ochotona princeps ENSOPRG000000133352 retrocopies
retro_opri_719, retro_opri_974,
Procavia capensis ENSPCAG000000064283 retrocopies
retro_pcap_129, retro_pcap_307, retro_pcap_373,
Pongo abelii ENSPPYG000000013532 retrocopies
retro_pabe_1850, retro_pabe_3010,
Pan troglodytes ENSPTRG000000007353 retrocopies
retro_ptro_1459, retro_ptro_1658, retro_ptro_2489,
Rattus norvegicus ENSRNOG000000085128 retrocopies
retro_rnor_1113, retro_rnor_1666, retro_rnor_1870, retro_rnor_1871, retro_rnor_1872, retro_rnor_537, retro_rnor_760, retro_rnor_998,
Sorex araneus ENSSARG000000031732 retrocopies
retro_sara_680, retro_sara_690,
Ictidomys tridecemlineatus ENSSTOG000000061296 retrocopies
retro_itri_1309, retro_itri_402, retro_itri_459, retro_itri_541, retro_itri_701, retro_itri_810,
Tupaia belangeri ENSTBEG0000001330730 retrocopies
retro_tbel_1050, retro_tbel_1052, retro_tbel_1178, retro_tbel_1595, retro_tbel_1642, retro_tbel_1785, retro_tbel_1883, retro_tbel_1924, retro_tbel_2245, retro_tbel_2290, retro_tbel_2532, retro_tbel_2979, retro_tbel_3092, retro_tbel_3100, retro_tbel_3340, retro_tbel_3469, retro_tbel_3483, retro_tbel_3520, retro_tbel_3583, retro_tbel_3598, retro_tbel_3986, retro_tbel_4045, retro_tbel_4278, retro_tbel_4283, retro_tbel_4563, retro_tbel_4623, retro_tbel_539, retro_tbel_701, retro_tbel_98, retro_tbel_991,
Tarsius syrichta ENSTSYG000000136353 retrocopies
retro_tsyr_1576, retro_tsyr_1822, retro_tsyr_2045,


Copyright © RetrogeneDB 2014-2017