RetrogeneDB ID:

retro_mmul_1810

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:4:159375290..159376153(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.3111
Ensembl ID:ENSMMUG00000002163
Aliases:None
Description:keratin, type II cytoskeletal 8 [Source:RefSeq peptide;Acc:NP_001247474]


Retrocopy-Parental alignment summary:






>retro_mmul_1810
ATGTCCGTCAGGGTGACCCAGAAGTCCTACAAGGTGTCCACTTCTGGCCCCCTGGCTTTCAGCAGCTGCTCCTACATGAG
TGGGCCCAGTGCCCACATCACCTCCTCAAGTTTCAGCCAAGTGGGCAGCAGCAGCTTCTGGGAGTGGCCCGGGTGGAGGC
TATGGTGGGGCCAGCAGCATGGGAAGCATCACTGCCGTCATGGTCAACCAGAGCCTGCTGAGCTCCCTTGACCTGGAGGT
GGACCCCAATGTCCAGGCCATGCGCACCAAGGAGAAGGAGTATATCAAGACCCTCAACAAGTTTGCCTCCTTCATAGACA
AGGTACAATTCCTGGAGCAGCAGAACAAGATGCTGGAGACCAAGTGGAGCCTCAGAAGCACCAGAAGATGGCTCGGAGCA
ACATGGACAACATGTTCAAGAGCTACATCAACAACCCTAGGCAGCAGCCAGACACTGTGGGCCAGGAGAAGCTGAGCTTG
AGGCAGAGCTTGGCAACATGCAGCGGCTGGTGGAGGACTTTAAGAACAAGTACAAGGATGAGATCAATAAGCATACAGAC
ATGGAGAATGAATTTGTCCTCATCAAGAAGGACATGGATGATGCTTACATGAACCAGGTAGAGTTGGAGTCTCACCTGGA
AGGGCTGACTGATGAGATCAATTTCCTCAGGCAGCTGTATGAAGAGGAGATCCAGGAGCTGCAGTCCCAGATCTCAGACA
CATCTGTGGTGCTGTCCATGGACAACAGCCACTCCCTGGACACGGACAGTATCATCGCTGAGGTCAAGGTGCGGTAGGAG
GAGATCGCTAACTACAGCCATGCTGAGGCTGAAAGCATGTACCAGATCAAGTATGCAAACCTA

ORF - retro_mmul_1810 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.51 %
Parental protein coverage: 59.83 %
Number of stop codons detected: 1
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMSIRVTQKSYKVSTSGPRAFSSRSYTSGPGARISSSSFSRVGSSSF-RGGLGGGYGGASGMGGITAVTVN
MS.RVTQKSYKVSTSGP.AFSS.SY.SGP.A.I.SSSFS.VGSSSF...G.GGGYGGAS.MG.ITAV.VN
RetrocopyMSVRVTQKSYKVSTSGPLAFSSCSYMSGPSAHITSSSFSQVGSSSF>GSGPGGGYGGASSMGSITAVMVN
ParentalQSLLSPLNLEVDPNIQAVRTQEKEQIKTLNNKFASFIDKVRFLEQQNKMLETKWSLL-QQQKTARSNMDN
QSLLS.L.LEVDPN.QA.RT.EKE.IKTLN.KFASFIDKV.FLEQQNKMLETKWSL....QK.ARSNMDN
RetrocopyQSLLSSLDLEVDPNVQAMRTKEKEYIKTLN-KFASFIDKVQFLEQQNKMLETKWSLR<KHQKMARSNMDN
ParentalMFESYINNLRRQLETLGQEKL-KLEAELGNMQGLVEDFKNKYEDEINKRTEMENEFVLIKKDVDEAYMNK
MF.SYINN.R.Q..T.GQEKL..LEAELGNMQ.LVEDFKNKY.DEINK.T.MENEFVLIKKD.D.AYMN.
RetrocopyMFKSYINNPRQQPDTVGQEKL<ELEAELGNMQRLVEDFKNKYKDEINKHTDMENEFVLIKKDMDDAYMNQ
ParentalVELESRLEGLTDEINFLRQLYEEEIRELQSQISDTSVVLSMDNSRSLDMDSIIAEVKAQYEEIANRSRAE
VELES.LEGLTDEINFLRQLYEEEI.ELQSQISDTSVVLSMDNS.SLD.DSIIAEVK...EEIAN.S.AE
RetrocopyVELESHLEGLTDEINFLRQLYEEEIQELQSQISDTSVVLSMDNSHSLDTDSIIAEVKVR*EEIANYSHAE
ParentalAESMYQIKYEEL
AESMYQIKY..L
RetrocopyAESMYQIKYANL

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 .11 RPM 0 .00 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 0 .24 RPM
SRP007412_cerebellum 0 .00 RPM 0 .06 RPM
SRP007412_heart 0 .06 RPM 8 .24 RPM
SRP007412_kidney 0 .00 RPM 22 .18 RPM
SRP007412_liver 0 .00 RPM 33 .41 RPM
SRP007412_testis 0 .04 RPM 0 .94 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_1810 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1810 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1810 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 151 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000071992 retrocopies
retro_cfam_1036, retro_cfam_1590,
Callithrix jacchus ENSCJAG000000181473 retrocopies
retro_cjac_124, retro_cjac_167, retro_cjac_216,
Cavia porcellus ENSCPOG000000026155 retrocopies
retro_cpor_1269, retro_cpor_1459, retro_cpor_233, retro_cpor_302, retro_cpor_516,
Dasypus novemcinctus ENSDNOG000000074003 retrocopies
retro_dnov_1267, retro_dnov_1886, retro_dnov_2358,
Felis catus ENSFCAG000000002982 retrocopies
retro_fcat_1142, retro_fcat_891,
Homo sapiens ENSG0000017042128 retrocopies
retro_hsap_1012, retro_hsap_1024, retro_hsap_1324, retro_hsap_1513, retro_hsap_1557, retro_hsap_1599, retro_hsap_169, retro_hsap_1708, retro_hsap_235, retro_hsap_2354, retro_hsap_2669, retro_hsap_2731, retro_hsap_2768, retro_hsap_2797, retro_hsap_2842, retro_hsap_3069, retro_hsap_3359, retro_hsap_3379, retro_hsap_3433, retro_hsap_371, retro_hsap_3963, retro_hsap_4203, retro_hsap_4688, retro_hsap_4691, retro_hsap_4775, retro_hsap_644, retro_hsap_844, retro_hsap_932,
Gorilla gorilla ENSGGOG0000001467318 retrocopies
retro_ggor_1160, retro_ggor_1787, retro_ggor_1862, retro_ggor_1897, retro_ggor_1900, retro_ggor_2320, retro_ggor_2662, retro_ggor_2913, retro_ggor_2918, retro_ggor_297, retro_ggor_2975, retro_ggor_382, retro_ggor_564, retro_ggor_66, retro_ggor_691, retro_ggor_751, retro_ggor_803, retro_ggor_809,
Macaca mulatta ENSMMUG00000002163 22 retrocopies
retro_mmul_1069, retro_mmul_1122, retro_mmul_1178, retro_mmul_1349, retro_mmul_1351, retro_mmul_1412, retro_mmul_1697, retro_mmul_1753, retro_mmul_1810 , retro_mmul_1855, retro_mmul_1866, retro_mmul_2097, retro_mmul_2137, retro_mmul_2357, retro_mmul_2431, retro_mmul_2546, retro_mmul_289, retro_mmul_488, retro_mmul_58, retro_mmul_766, retro_mmul_816, retro_mmul_886,
Mustela putorius furoENSMPUG000000064417 retrocopies
retro_mputfur_1101, retro_mputfur_1208, retro_mputfur_1271, retro_mputfur_1557, retro_mputfur_1587, retro_mputfur_556, retro_mputfur_895,
Mus musculus ENSMUSG000000493821 retrocopy
retro_mmus_2905,
Nomascus leucogenys ENSNLEG000000177338 retrocopies
retro_nleu_1913, retro_nleu_225, retro_nleu_2285, retro_nleu_2421, retro_nleu_2485, retro_nleu_2727, retro_nleu_2787, retro_nleu_672,
Oryctolagus cuniculus ENSOCUG000000069451 retrocopy
retro_ocun_313,
Otolemur garnettii ENSOGAG0000001174016 retrocopies
retro_ogar_1076, retro_ogar_1162, retro_ogar_1256, retro_ogar_1572, retro_ogar_1874, retro_ogar_1898, retro_ogar_1952, retro_ogar_2004, retro_ogar_2149, retro_ogar_2177, retro_ogar_2261, retro_ogar_2500, retro_ogar_3198, retro_ogar_3318, retro_ogar_339, retro_ogar_664,
Pongo abelii ENSPPYG0000000456231 retrocopies
retro_pabe_1102, retro_pabe_1261, retro_pabe_1289, retro_pabe_1460, retro_pabe_1743, retro_pabe_2063, retro_pabe_2077, retro_pabe_2129, retro_pabe_2142, retro_pabe_2214, retro_pabe_2270, retro_pabe_2352, retro_pabe_2544, retro_pabe_2741, retro_pabe_2763, retro_pabe_2787, retro_pabe_2842, retro_pabe_2926, retro_pabe_2943, retro_pabe_3138, retro_pabe_332, retro_pabe_3439, retro_pabe_3644, retro_pabe_3716, retro_pabe_417, retro_pabe_460, retro_pabe_569, retro_pabe_605, retro_pabe_701, retro_pabe_803, retro_pabe_851,
Pteropus vampyrus ENSPVAG000000093603 retrocopies
retro_pvam_1299, retro_pvam_1396, retro_pvam_45,
Rattus norvegicus ENSRNOG000000097791 retrocopy
retro_rnor_807,


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