RetrogeneDB ID:

retro_mmul_1788

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:4:114188297..114188958(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.2964
Ensembl ID:ENSMMUG00000014493
Aliases:None
Description:U2 small nuclear ribonucleoprotein B'' [Source:RefSeq peptide;Acc:NP_001247823]


Retrocopy-Parental alignment summary:






>retro_mmul_1788
ATGGGTATCAGACCAAATCATACAATTTATATCAACAATGTGAATGGCAAAATTAAAAAGGAAGAATTGAAGAGATCCCT
ATATGCCCTGTTTTCTTAGTTTGGTCATGTGGTGGACTTTGTGGCTTTAAGGACCATGAAGATGAAGGGCAGGCCTTTGT
CATATTTAAGGAACTGGGCTCATCCACAAGTGCTTTGAGACAGTCACAAGGATTTCCATTTCATGGTAAACCAATGTGAA
TATATATGCAAAAACAGATTCGGATATAATATCTAAAATGTGCGGCACTTTTGCTGACAAAGAAAAGAAGAAGGGCAAAA
CTGTGGAATAGACTGCAACCACCACAAACAAAAGGCCTGGCTAGGGAACTCCAAATTCAGCTAATATCCAAGGAAATTCA
ACACCAAATCCTCAGGTCCTTGATTATCCTCCAAACTATATTTTATTCCTTAATAACTTACCAGAAGAGACTAATGAGAT
GATGTTATCCATGCTGTTTAATCAGTTCCCTGGCTTCAAGGAAGTATGTCTAGTACCAGGGAGGCATGACATTGCTTTTG
TTGAATTTGAAAATGATGGTCAGGCTGGAGCTGCCAGGGATGCTTTGCAGGGATTTAAGATCACAACATCCCATGCTATG
AAGATCACCTATGCCAAGAAA

ORF - retro_mmul_1788 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.22 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRG-QAFVIFKELGSSTNALRQL
M.IRPNHTIYINN.N.KIKKEELKRSLYALFS.FGHVVD.VAL.TMKM.G.QAFVIFKELGSST.ALRQ.
RetrocopyMGIRPNHTIYINNVNGKIKKEELKRSLYALFS*FGHVVDFVALRTMKMKG<QAFVIFKELGSSTSALRQS
ParentalQGFPFYGKPMRIQ-YAKTDSDIISKMRGTFADKEKKKEKKKAKAVEQTATTTNKKPGQGTPNSANTQGNT
QGFPF.GKPM.I..YAKTDSDIISKM.GTFAD....KEKKK.K.VE.TATTTNK.PG.GTPNSAN.QGN.
RetrocopyQGFPFHGKPM*IY<YAKTDSDIISKMCGTFAD----KEKKKGKTVE*TATTTNKRPG*GTPNSANIQGNS
ParentalTPNPQVPDYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDALQ
TPNPQV.DYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEV.LVPGRHDIAFVEFENDGQAGAARDALQ
RetrocopyTPNPQVLDYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVCLVPGRHDIAFVEFENDGQAGAARDALQ
ParentalGFKITPSHAMKITYAKK
GFKIT.SHAMKITYAKK
RetrocopyGFKITTSHAMKITYAKK

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 0 .00 RPM 22 .41 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 11 .66 RPM
SRP007412_cerebellum 0 .00 RPM 24 .47 RPM
SRP007412_heart 0 .00 RPM 12 .19 RPM
SRP007412_kidney 0 .00 RPM 16 .55 RPM
SRP007412_liver 0 .08 RPM 4 .47 RPM
SRP007412_testis 0 .00 RPM 22 .99 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_1788 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1788 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1788 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 27 parental genes, and 118 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000165002 retrocopies
retro_amel_235, retro_amel_490,
Bos taurus ENSBTAG000000275061 retrocopy
retro_btau_1172,
Canis familiaris ENSCAFG000000055204 retrocopies
retro_cfam_1097, retro_cfam_1661, retro_cfam_1689, retro_cfam_264,
Callithrix jacchus ENSCJAG000000048111 retrocopy
retro_cjac_269,
Equus caballus ENSECAG000000184072 retrocopies
retro_ecab_118, retro_ecab_372,
Echinops telfairi ENSETEG000000010853 retrocopies
retro_etel_1283, retro_etel_1723, retro_etel_2031,
Felis catus ENSFCAG000000261151 retrocopy
retro_fcat_1513,
Homo sapiens ENSG000001258702 retrocopies
retro_hsap_3678, retro_hsap_732,
Gorilla gorilla ENSGGOG000000039372 retrocopies
retro_ggor_2487, retro_ggor_617,
Macropus eugenii ENSMEUG000000165522 retrocopies
retro_meug_465, retro_meug_482,
Microcebus murinus ENSMICG000000154041 retrocopy
retro_mmur_762,
Myotis lucifugus ENSMLUG000000081635 retrocopies
retro_mluc_1450, retro_mluc_1451, retro_mluc_1452, retro_mluc_2268, retro_mluc_586,
Macaca mulatta ENSMMUG00000014493 1 retrocopy
retro_mmul_1788 ,
Mus musculus ENSMUSG000000083334 retrocopies
retro_mmus_1496, retro_mmus_1497, retro_mmus_2378, retro_mmus_3325,
Nomascus leucogenys ENSNLEG000000096232 retrocopies
retro_nleu_477, retro_nleu_527,
Oryctolagus cuniculus ENSOCUG000000014273 retrocopies
retro_ocun_1069, retro_ocun_380, retro_ocun_485,
Otolemur garnettii ENSOGAG000000151461 retrocopy
retro_ogar_2042,
Ochotona princeps ENSOPRG000000115872 retrocopies
retro_opri_59, retro_opri_776,
Pongo abelii ENSPPYG000000107231 retrocopy
retro_pabe_630,
Pan troglodytes ENSPTRG000000132712 retrocopies
retro_ptro_2492, retro_ptro_520,
Rattus norvegicus ENSRNOG000000049671 retrocopy
retro_rnor_962,
Sorex araneus ENSSARG0000000268114 retrocopies
retro_sara_197, retro_sara_209, retro_sara_289, retro_sara_290, retro_sara_328, retro_sara_374, retro_sara_514, retro_sara_546, retro_sara_548, retro_sara_604, retro_sara_670, retro_sara_724, retro_sara_733, retro_sara_770,
Ictidomys tridecemlineatus ENSSTOG000000091981 retrocopy
retro_itri_1895,
Tupaia belangeri ENSTBEG000000128926 retrocopies
retro_tbel_1123, retro_tbel_2350, retro_tbel_3126, retro_tbel_3534, retro_tbel_3754, retro_tbel_530,
Tarsius syrichta ENSTSYG0000000885752 retrocopies
retro_tsyr_1067, retro_tsyr_1072, retro_tsyr_1083, retro_tsyr_1124, retro_tsyr_1158, retro_tsyr_1175, retro_tsyr_1216, retro_tsyr_1223, retro_tsyr_1242, retro_tsyr_1244, retro_tsyr_1245, retro_tsyr_1247, retro_tsyr_1261, retro_tsyr_1279, retro_tsyr_1323, retro_tsyr_1339, retro_tsyr_1361, retro_tsyr_1386, retro_tsyr_1434, retro_tsyr_1438, retro_tsyr_1461, retro_tsyr_1468, retro_tsyr_1469, retro_tsyr_1470, retro_tsyr_1501, retro_tsyr_1503, retro_tsyr_1513, retro_tsyr_1533, retro_tsyr_1586, retro_tsyr_1599, retro_tsyr_1616, retro_tsyr_1619, retro_tsyr_1629, retro_tsyr_1699, retro_tsyr_1720, retro_tsyr_1724, retro_tsyr_1776, retro_tsyr_1872, retro_tsyr_1930, retro_tsyr_1962, retro_tsyr_286, retro_tsyr_384, retro_tsyr_397, retro_tsyr_500, retro_tsyr_584, retro_tsyr_629, retro_tsyr_695, retro_tsyr_805, retro_tsyr_835, retro_tsyr_899, retro_tsyr_977, retro_tsyr_979,
Tursiops truncatus ENSTTRG000000063951 retrocopy
retro_ttru_1545,
Vicugna pacos ENSVPAG000000045571 retrocopy
retro_vpac_67,


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