RetrogeneDB ID:

retro_ocun_363

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:1:54523390..54524281(-)
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:ENSOCUG00000004642
Aliases:None
Description:ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 [Source:HGNC Symbol;Acc:833]


Retrocopy-Parental alignment summary:






>retro_ocun_363
ATGTTTTCTCAGGTGAGCATCGCTGGGCTGTCGGCCAGGGCCTTGCAACCGCAATGAGTCCAAGTTCGAAACATGGCAAC
TTTGAAAGACATTACCAGGTGACTAAAGTCAATTAAAAACATCCAAAAAATTACCAAGCCTATGAAAATGGTGGCAGCAG
CAAAATATGCCCCAGTTGAGAGGAAGCTGAAACTAGCTTGAGTGTATGGAATAGGATTTTTTTGCTCTGACTGAAAAAGC
TCATATTAAGGCACCTGAACACAAGAAGAAACACCTCCTTATTGGTATGCCTCAGATCAAGGGCTTTGTGGTGCTATCAT
TCCTCCATTGCCAAACAGATGAAAAGTGAGGTGGCTACACTCACAGCCGCCAGAAGAGAAGTTTTGCTGGTTGGAACTGG
TGACAAAATCAGGGGCATACTTCATAGGACTCATTCTGACCAGTTTCTAGTAACATTCAAAGAAGTTGGAAGAAAGCCCC
CTACTTTTGGAGATGTGTCAGTCATTGCTCTTGAATTACTAATCTCTGGATACAAGTTTGATGAAGGGTCTATCATCTTT
AATCGATTAAAGTCTGTAATCTCCTACAAAACAGAAGAAAAGCCAACTTTTTCCCTTAATACCATTGCAAGTGCTGAGAG
CATGAGTATCTATGATGATGCTGATGCTGATGTGATGCAAAATTACCAAGAATACAATTTGGCCAACATCTTCTACTACT
CTCTGAAGGAGTCCACCACCAGTGAGCAGAGTGTGAGAATGACAGCTGTGGACAAGGCCAGCAAGAATGCTTCTGAGATG
ATTCACAAAACTGACTCTGACATTCAACCGTAACCCACCAAGCTGTCATCACAAAAGAGTAGACTGAAATTATCTTGGTG
CTGCAGCTCTG

ORF - retro_ocun_363 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.85 %
Parental protein coverage: 99.66 %
Number of stop codons detected: 4
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalMFSRASVAGLSARALQPQWVQVRNMATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYG
MFS..S.AGLSARALQPQ.VQVRNMATLKDITR.LKSIKNIQKITK.MKMVAAAKYA..ER.LK.A.VYG
RetrocopyMFSQVSIAGLSARALQPQ*VQVRNMATLKDITR*LKSIKNIQKITKPMKMVAAAKYAPVERKLKLA*VYG
ParentalIGSL-ALYEKADIKAPEDKKKHLLIGV-SSDRGLCGAI-HSSVAKQMKSEVAALTAAGKEVMLVGVGDKI
IG...AL.EKA.IKAPE.KKKHLLIG...SD.GLCGAI.HSS.AKQMKSEVA.LTAA..EV.LVG.GDKI
RetrocopyIGFF>ALTEKAHIKAPEHKKKHLLIGM<ASDQGLCGAI<HSSIAKQMKSEVATLTAARREVLLVGTGDKI
ParentalRGILHRTHSDQFLVTFKEVGRKPPTFGDASVIALELLNSGYEFDEGSIIFNRFKSVISYKTEEKPIFSLN
RGILHRTHSDQFLVTFKEVGRKPPTFGD.SVIALELL.SGY.FDEGSIIFNR.KSVISYKTEEKP.FSLN
RetrocopyRGILHRTHSDQFLVTFKEVGRKPPTFGDVSVIALELLISGYKFDEGSIIFNRLKSVISYKTEEKPTFSLN
ParentalTIASAESMSIYDDVDADVLQNYQEYNLANIIYYSLKESTTSEQSARMTAMDNASKNASEMI-DKLTLTFN
TIASAESMSI..........NYQEYNLANI.YYSLKESTTSEQS.RMTA.D.ASKNASEMI..KLTLTFN
RetrocopyTIASAESMSIXXXXXXXXXXNYQEYNLANIFYYSLKESTTSEQSVRMTAVDKASKNASEMI>TKLTLTFN
ParentalR-TRQAVITKELIEII-SGAAAL
R.T.QAVITKE..EII..GAAAL
RetrocopyR>THQAVITKE*TEII<LGAAAL

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
SRP017611_brain 0 .06 RPM 190 .12 RPM
SRP017611_kidney 0 .00 RPM 432 .89 RPM
SRP017611_liver 0 .00 RPM 84 .24 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_363 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_363 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_363 has 0 orthologous retrocopies within eutheria group .

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 ENSOCUG00000004642 2 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 ENSPPYG000000020761 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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