RetrogeneDB ID:

retro_ptro_1974

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:4:37953902..37954509(+)
Located in intron of:ENSPTRG00000015981
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PTTG1
Ensembl ID:ENSPTRG00000017492
Aliases:PTTG1, Securin
Description:Pan troglodytes pituitary tumor-transforming 1 (PTTG1), mRNA. [Source:RefSeq mRNA;Acc:NM_001135616]


Retrocopy-Parental alignment summary:






>retro_ptro_1974
ATGGCTACTCTGATCTATGTTGATAAGGAAATTGGAGAACCAGGCACCCGTGTGGCTGCTAAGGATGTGCTGAAGCTGGA
GTCTAGACCTTCAATCAAAGCATTAGATGGGATATCTCAAGTTTTAACACCACGTTTTGGCAAAACATACGATGCTCCAT
CAGCCTTACCTAAAGCTACCAGAAAGGCTTTGGGCACTGTCAACAGAGCTACAGAAAAGTCAGTAAAGACCAATGGACCC
AGAAAACAAAAACAGCCAAGCTTTTCTGCCAAAAAGATGACCGAGAAGACTGTTAAAACAAAAAGCTCTGTTCCTGCCTC
AGATGACGCCTATCCAGAAACAGAAAAATTCTTTCCCTTCAATCTTCTAGACTTTGAGAGTTTTGACCTGCCTGAAGAGC
ACCAGATTGCACACCTCCCCTTGAGTGGAGTGCCTCTCATGATCCTTGATGAGGAGGGAGAGCTTGAAAAGCTGTTTCAG
CTGGGACCCCCTTCACCTGTGAGAATGCCCTCTCCACCATGGGAATGCAATCTGTTTGCAGTCTCCTTCAAGCATTCTGT
CGACCCTGGATGTTGAATTGCCAGCTGTTTGCTATGACATAGATATT

ORF - retro_ptro_1974 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.64 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMATLIYVDKENGEPGTRVAAKDGLKLGSGPSIKALDGRSQVSTPRFGKTFDAPPALPKATRKALGTVNRA
MATLIYVDKE.GEPGTRVAAKD.LKL.S.PSIKALDG.SQV.TPRFGKT.DAP.ALPKATRKALGTVNRA
RetrocopyMATLIYVDKEIGEPGTRVAAKDVLKLESRPSIKALDGISQVLTPRFGKTYDAPSALPKATRKALGTVNRA
ParentalTEKSVKTKGPLKQKQPSFSAKKMTEKTVKAKSSVPASDDAYPEIEKFFPFNPLDFESFDLPEEHQIAHLP
TEKSVKT.GP.KQKQPSFSAKKMTEKTVK.KSSVPASDDAYPE.EKFFPFN.LDFESFDLPEEHQIAHLP
RetrocopyTEKSVKTNGPRKQKQPSFSAKKMTEKTVKTKSSVPASDDAYPETEKFFPFNLLDFESFDLPEEHQIAHLP
ParentalLSGVPLMILDEERELEKLFQLGPPSPVKMPSPPWESNL-LQSPSSILSTLDVELPPVCCDIDI
LSGVPLMILDEE.ELEKLFQLGPPSPV.MPSPPWE.NL.LQSPSSILSTLDVELP.VC.DIDI
RetrocopyLSGVPLMILDEEGELEKLFQLGPPSPVRMPSPPWECNL>LQSPSSILSTLDVELPAVCYDIDI

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_prefrontal_cortex 0 .05 RPM 1 .68 RPM
SRP007412_cerebellum 0 .18 RPM 2 .01 RPM
SRP007412_heart 0 .06 RPM 0 .41 RPM
SRP007412_kidney 0 .08 RPM 0 .84 RPM
SRP007412_liver 0 .00 RPM 3 .40 RPM
SRP007412_testis 0 .11 RPM 143 .95 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_1974 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1974 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1974 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_67
Gorilla gorilla retro_ggor_2022
Pongo abelii retro_pabe_2428
Callithrix jacchus retro_cjac_2293
Parental genes homology:
Parental genes homology involve 26 parental genes, and 72 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000121842 retrocopies
retro_btau_122, retro_btau_53,
Canis familiaris ENSCAFG000000172641 retrocopy
retro_cfam_1586,
Choloepus hoffmanni ENSCHOG0000000946411 retrocopies
retro_chof_1246, retro_chof_1518, retro_chof_1679, retro_chof_2027, retro_chof_2161, retro_chof_2304, retro_chof_2459, retro_chof_2463, retro_chof_2690, retro_chof_426, retro_chof_526,
Callithrix jacchus ENSCJAG000000191654 retrocopies
retro_cjac_2184, retro_cjac_2293, retro_cjac_2530, retro_cjac_3062,
Cavia porcellus ENSCPOG000000119712 retrocopies
retro_cpor_1151, retro_cpor_820,
Dasypus novemcinctus ENSDNOG000000240804 retrocopies
retro_dnov_1400, retro_dnov_2553, retro_dnov_918, retro_dnov_949,
Dipodomys ordii ENSDORG000000079681 retrocopy
retro_dord_779,
Felis catus ENSFCAG000000240743 retrocopies
retro_fcat_1153, retro_fcat_846, retro_fcat_878,
Homo sapiens ENSG000001646114 retrocopies
retro_hsap_3823, retro_hsap_4068, retro_hsap_67, retro_hsap_881,
Gorilla gorilla ENSGGOG000000169375 retrocopies
retro_ggor_2022, retro_ggor_2572, retro_ggor_2573, retro_ggor_2731, retro_ggor_714,
Loxodonta africana ENSLAFG000000111351 retrocopy
retro_lafr_258,
Macropus eugenii ENSMEUG000000059931 retrocopy
retro_meug_577,
Microcebus murinus ENSMICG000000063631 retrocopy
retro_mmur_181,
Myotis lucifugus ENSMLUG000000023171 retrocopy
retro_mluc_1080,
Macaca mulatta ENSMMUG000000230773 retrocopies
retro_mmul_1052, retro_mmul_1629, retro_mmul_2347,
Mustela putorius furoENSMPUG000000132413 retrocopies
retro_mputfur_1358, retro_mputfur_429, retro_mputfur_813,
Nomascus leucogenys ENSNLEG000000043965 retrocopies
retro_nleu_218, retro_nleu_2487, retro_nleu_2527, retro_nleu_2528, retro_nleu_830,
Oryctolagus cuniculus ENSOCUG000000148772 retrocopies
retro_ocun_150, retro_ocun_1565,
Otolemur garnettii ENSOGAG000000123072 retrocopies
retro_ogar_2802, retro_ogar_990,
Pongo abelii ENSPPYG000000160094 retrocopies
retro_pabe_2428, retro_pabe_3071, retro_pabe_3341, retro_pabe_674,
Pan troglodytes ENSPTRG00000017492 4 retrocopies
retro_ptro_1974 , retro_ptro_2601, retro_ptro_2757, retro_ptro_610,
Pteropus vampyrus ENSPVAG000000159382 retrocopies
retro_pvam_431, retro_pvam_704,
Sarcophilus harrisii ENSSHAG000000102671 retrocopy
retro_shar_104,
Tupaia belangeri ENSTBEG000000159662 retrocopies
retro_tbel_2399, retro_tbel_771,
Tursiops truncatus ENSTTRG000000115701 retrocopy
retro_ttru_259,
Vicugna pacos ENSVPAG000000095942 retrocopies
retro_vpac_178, retro_vpac_33,


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