RetrogeneDB ID:

retro_mmul_1465

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:2:137037028..137037280(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.633
Ensembl ID:ENSMMUG00000000869
Aliases:None
Description:U1 small nuclear ribonucleoprotein C [Source:UniProtKB/Swiss-Prot;Acc:F6TFD9]


Retrocopy-Parental alignment summary:






>retro_mmul_1465
ATGCCTAAGTTTTGTTGTGACTTCTGCAATACATACCTCACCCATGCCTGTCCATCTGTGGGAACCTACCACTGCAGTGG
GAGGAAACACAAAGAGAATGTGAAAGACTACTACCAGAAATGGATGGAACAGCAGGCTCGGAGCCTGGCTGACAGAACAA
AGACTGCATCTCAACAAGGAAGAACACCTCCGACTCTGTTCTCTGCTCCTCTTCCTGCAGGGGCGATGATCCAACCTCTC
CCACCCGGGCTC

ORF - retro_mmul_1465 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.81 %
Parental protein coverage: 52.2 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPFSAP
MPKF.CD.C.TYLTH..PSV...HCSGRKHKENVKDYYQKWME.QA.SL.D.T..A.QQG..PPT.FSAP
RetrocopyMPKFCCDFCNTYLTHACPSVGTYHCSGRKHKENVKDYYQKWMEQQARSLADRTKTASQQGRTPPTLFSAP
ParentalPPAGAMIPP-PPSL
.PAGAMI.P.PP.L
RetrocopyLPAGAMIQPLPPGL

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 3 .47 RPM
SRP007412_brain_prefrontal_cortex 0 .08 RPM 13 .17 RPM
SRP007412_cerebellum 0 .06 RPM 4 .00 RPM
SRP007412_heart 0 .00 RPM 5 .12 RPM
SRP007412_kidney 0 .12 RPM 5 .16 RPM
SRP007412_liver 0 .08 RPM 5 .11 RPM
SRP007412_testis 0 .04 RPM 18 .58 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_1465 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1465 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1465 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2865
Pan troglodytes retro_ptro_1937
Gorilla gorilla retro_ggor_1981
Pongo abelii retro_pabe_2367
Parental genes homology:
Parental genes homology involve 20 parental genes, and 108 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000009637 retrocopies
retro_amel_1237, retro_amel_1249, retro_amel_149, retro_amel_1522, retro_amel_1523, retro_amel_592, retro_amel_988,
Canis familiaris ENSCAFG000000012313 retrocopies
retro_cfam_348, retro_cfam_402, retro_cfam_409,
Callithrix jacchus ENSCJAG0000001532116 retrocopies
retro_cjac_1009, retro_cjac_1015, retro_cjac_1064, retro_cjac_1750, retro_cjac_1937, retro_cjac_2014, retro_cjac_2395, retro_cjac_2456, retro_cjac_2785, retro_cjac_3056, retro_cjac_3110, retro_cjac_400, retro_cjac_4010, retro_cjac_617, retro_cjac_770, retro_cjac_873,
Cavia porcellus ENSCPOG000000085633 retrocopies
retro_cpor_1529, retro_cpor_1540, retro_cpor_288,
Felis catus ENSFCAG0000000587612 retrocopies
retro_fcat_1008, retro_fcat_1088, retro_fcat_1265, retro_fcat_1545, retro_fcat_1599, retro_fcat_161, retro_fcat_1664, retro_fcat_1814, retro_fcat_446, retro_fcat_578, retro_fcat_627, retro_fcat_922,
Gorilla gorilla ENSGGOG000000124997 retrocopies
retro_ggor_1169, retro_ggor_1333, retro_ggor_1364, retro_ggor_1981, retro_ggor_2577, retro_ggor_2699, retro_ggor_2842,
Myotis lucifugus ENSMLUG000000024888 retrocopies
retro_mluc_1246, retro_mluc_1627, retro_mluc_2020, retro_mluc_2099, retro_mluc_2144, retro_mluc_2332, retro_mluc_735, retro_mluc_962,
Macaca mulatta ENSMMUG00000000869 9 retrocopies
retro_mmul_1148, retro_mmul_1161, retro_mmul_1343, retro_mmul_1465 , retro_mmul_1573, retro_mmul_1626, retro_mmul_2016, retro_mmul_2314, retro_mmul_678,
Monodelphis domestica ENSMODG000000139041 retrocopy
retro_mdom_22,
Mustela putorius furoENSMPUG000000032107 retrocopies
retro_mputfur_1233, retro_mputfur_1260, retro_mputfur_1396, retro_mputfur_374, retro_mputfur_441, retro_mputfur_519, retro_mputfur_531,
Nomascus leucogenys ENSNLEG000000083922 retrocopies
retro_nleu_2129, retro_nleu_99,
Oryctolagus cuniculus ENSOCUG000000266683 retrocopies
retro_ocun_1019, retro_ocun_184, retro_ocun_196,
Otolemur garnettii ENSOGAG000000087559 retrocopies
retro_ogar_1040, retro_ogar_130, retro_ogar_1763, retro_ogar_183, retro_ogar_2434, retro_ogar_3064, retro_ogar_3322, retro_ogar_3377, retro_ogar_697,
Procavia capensis ENSPCAG000000168851 retrocopy
retro_pcap_34,
Pongo abelii ENSPPYG000000299023 retrocopies
retro_pabe_2367, retro_pabe_3397, retro_pabe_3524,
Pan troglodytes ENSPTRG000000180706 retrocopies
retro_ptro_1037, retro_ptro_1283, retro_ptro_1937, retro_ptro_2249, retro_ptro_2606, retro_ptro_2883,
Pteropus vampyrus ENSPVAG000000155971 retrocopy
retro_pvam_1213,
Sarcophilus harrisii ENSSHAG000000009451 retrocopy
retro_shar_112,
Ictidomys tridecemlineatus ENSSTOG000000137863 retrocopies
retro_itri_1278, retro_itri_1374, retro_itri_861,
Tarsius syrichta ENSTSYG000000112166 retrocopies
retro_tsyr_1198, retro_tsyr_1475, retro_tsyr_1746, retro_tsyr_185, retro_tsyr_260, retro_tsyr_690,


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