RetrogeneDB ID:

retro_pabe_1170

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:14:54518496..54519389(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP5C1
Ensembl ID:ENSPPYG00000002076
Aliases:None
Description:ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 [Source:HGNC Symbol;Acc:833]


Retrocopy-Parental alignment summary:






>retro_pabe_1170
GTGTTCTCTCACGTGGGCATCACTGGGCTGTTGGCCTGGACCTTGCAGCCACAATGGATTCAAGTTCGAAATATGGCAAC
TTTGAAAGATGTTACCAGGCGACTAAAGTCCATCAAAAACATCCAGAAAATTACCAAGTCTATGCAAATGGTAGCAGCAG
CAAAATACGCCCGAGCTGAGAGAGAGCTGAAACCAGCTTGAATATATGGATTGGGATCTTTGGCTCTGGAGAAAAAGCTG
GTATCAAGGTGCCTGAAGACAACAAGAAACACCTCCTTATTGGTGCATCCTCAGATCGAGGACTGTGTGGCGCTATTCAT
TCCTCCATTGCTAAACAGATGAAAAGCGAGGTTGCTACACTAACAGCAGCTGGGAAAGAAGTTATGCTTTTTGGAATTGG
TGACAAAATCAGGGGCATACTTTATAGGATGCATTCTGACCAGTTTCTGGTGGCATTAAAAGAAGTGAGAAGAAAGCCCC
CTACTTGTGGAGATGTGTCAGTCATTGCCCTTGAATTACTAAATTCTGGATATGAATTTGATGAAGGCTCCATCATCTTT
AATCAATTCAGGTCTGTCATCTCGTATAAGACTGAAGAAAAGCCCATCTTTTCGCTTAATACCATTGCAAGTGCCGAGAG
CATGAGTATCTACTATAATATTGATGCTGATGTGCTGCAAAATTACCAGGAATACAATCTGGCCAACAGCATCTACTACT
CTCTGAAGGAGTCCACAACTAGTGAGCAGAGTGCCAGGATGATAGCCATGGACAACACCAGCAAGAATGCTTCTGAGATG
ATTGACAAATTCACATTGACATTCAACTGTACCTGCCAAGCTGTCATCACAAAAGAGTTGACTGAAATTATCTTTGGTGC
TGTAGCTCTGGAT

ORF - retro_pabe_1170 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.96 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMFSRAGVAGLSAWTLQPQWIQVRNMATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARIYG
.FS..G..GL.AWTLQPQWIQVRNMATLKD.TRRLKSIKNIQKITKSM.MVAAAKYARAERELKPA.IYG
RetrocopyVFSHVGITGLLAWTLQPQWIQVRNMATLKDVTRRLKSIKNIQKITKSMQMVAAAKYARAERELKPA*IYG
ParentalLGSLALY-EKADIKGPEDKKKHLLIGVSSDRGLCGAIHSSIAKQMKSEVATLTAAGKEVMLVGVGDKIRG
LGSLAL..EKA.IK.PED.KKHLLIG.SSDRGLCGAIHSSIAKQMKSEVATLTAAGKEVML.G.GDKIRG
RetrocopyLGSLALE<EKAGIKVPEDNKKHLLIGASSDRGLCGAIHSSIAKQMKSEVATLTAAGKEVMLFGIGDKIRG
ParentalILYRTHSDQFLVAFKEVGRKPPTFGDASVIALELLNSGYEFDEGSIIFNKFRSVISYKTEEKPIFSLNTV
ILYR.HSDQFLVA.KEV.RKPPT.GD.SVIALELLNSGYEFDEGSIIFN.FRSVISYKTEEKPIFSLNT.
RetrocopyILYRMHSDQFLVALKEVRRKPPTCGDVSVIALELLNSGYEFDEGSIIFNQFRSVISYKTEEKPIFSLNTI
ParentalASADSMSIYDDIDADVLQNYQEYNLANIIYYSLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTR
ASA.SMSIY..IDADVLQNYQEYNLAN.IYYSLKESTTSEQSARM.AMDN.SKNASEMIDK.TLTFN.T.
RetrocopyASAESMSIYYNIDADVLQNYQEYNLANSIYYSLKESTTSEQSARMIAMDNTSKNASEMIDKFTLTFNCTC
ParentalQAVITKELIEIISGAAALD
QAVITKEL.EII.GA.ALD
RetrocopyQAVITKELTEIIFGAVALD

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 .06 RPM 47 .94 RPM
SRP007412_cerebellum 0 .00 RPM 65 .91 RPM
SRP007412_heart 0 .03 RPM 185 .71 RPM
SRP007412_kidney 0 .00 RPM 101 .56 RPM
SRP007412_liver 0 .12 RPM 68 .24 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_1170 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_1170 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1170 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1415
Pan troglodytes retro_ptro_968
Gorilla gorilla retro_ggor_1094
Parental genes homology:
Parental genes homology involve 21 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000050241 retrocopy
retro_cfam_1781,
Choloepus hoffmanni ENSCHOG000000112293 retrocopies
retro_chof_102, retro_chof_297, retro_chof_673,
Callithrix jacchus ENSCJAG000000206357 retrocopies
retro_cjac_1079, retro_cjac_1293, retro_cjac_1381, retro_cjac_1636, retro_cjac_2506, retro_cjac_4190, retro_cjac_526,
Cavia porcellus ENSCPOG000000105232 retrocopies
retro_cpor_422, retro_cpor_984,
Echinops telfairi ENSETEG000000105491 retrocopy
retro_etel_1406,
Felis catus ENSFCAG000000001961 retrocopy
retro_fcat_818,
Homo sapiens ENSG000001656291 retrocopy
retro_hsap_1415,
Gorilla gorilla ENSGGOG000000097191 retrocopy
retro_ggor_1094,
Macaca mulatta ENSMMUG000000092071 retrocopy
retro_mmul_2254,
Monodelphis domestica ENSMODG000000167201 retrocopy
retro_mdom_1287,
Mus musculus ENSMUSG000000257814 retrocopies
retro_mmus_1122, retro_mmus_2008, retro_mmus_3451, retro_mmus_3644,
Nomascus leucogenys ENSNLEG000000119171 retrocopy
retro_nleu_1836,
Oryctolagus cuniculus ENSOCUG000000046422 retrocopies
retro_ocun_1171, retro_ocun_363,
Otolemur garnettii ENSOGAG000000152422 retrocopies
retro_ogar_1099, retro_ogar_2738,
Procavia capensis ENSPCAG000000049711 retrocopy
retro_pcap_99,
Pongo abelii ENSPPYG00000002076 1 retrocopy
retro_pabe_1170 ,
Pan troglodytes ENSPTRG000000022771 retrocopy
retro_ptro_968,
Pteropus vampyrus ENSPVAG000000065123 retrocopies
retro_pvam_1466, retro_pvam_51, retro_pvam_530,
Ictidomys tridecemlineatus ENSSTOG000000261331 retrocopy
retro_itri_665,
Tupaia belangeri ENSTBEG000000115304 retrocopies
retro_tbel_1763, retro_tbel_2023, retro_tbel_4384, retro_tbel_4406,
Tarsius syrichta ENSTSYG000000030354 retrocopies
retro_tsyr_1268, retro_tsyr_1988, retro_tsyr_465, retro_tsyr_506,


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