RetrogeneDB ID:

retro_cpor_1239

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_6:46824950..46825433(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:C14ORF166
Ensembl ID:ENSCPOG00000001317
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_1239
ATGTTCCAATGCAAGCTGACAGCTCTCAACTACAAAACCCTGCTAGTTTCAACTGCAAAGATGAAACAGAAGTTAGAAAC
TTTATTGTTTGGCTTAAAAACCAGAAAATCAGACACAACAAGATTGAAGACAGGTAATTTATGAAACAACTCCAGCACTG
ACTAGTGCAAGTTCTTTGACAAGTATCTCAGAGATGTTGACTGTCCTTCCAAGATTCAGGCTCAACAAGAAGCAATTGAT
TGGCTCCTTGGCTTAGCTATTAGACTTGAATATGAAGATAATACTCAAAAATACAAGGACCTAGCACTTGATAACACATA
AAATACTGACAATGCAACTAAAAATGCAGAGCCATTGATCAATTCGAGTGTAAATAATCCCAATTTGAATGCTGGCATAA
AGGCTTTAGCTAACCTCCTTCAGATTCAGTGCCATGATGACTACCTGGTAATACATAAGATAATTCACATTTTGGTTCAG
GAG

ORF - retro_cpor_1239 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.8 %
Parental protein coverage: 66.39 %
Number of stop codons detected: 3
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMFRRKLTALDY-HNPAGFNC-KDETEFRNFIVWLEDQKIRHYKIEDRGNLRNIPSSDWPKFFEKYLRDVD
MF..KLTAL.Y..NPA.FNC.K...........L...K.........GNL.N..S.D..KFF.KYLRDVD
RetrocopyMFQCKLTALNY<QNPASFNC>KMKQKLETLLFGLKTRKSDTTRLKT-GNL*NNSSTD*CKFFDKYLRDVD
ParentalCPFKIQDRQEAIDWLLGLAVRLEYGDNAEKYKDLTPDNAKNIDNATKNAEPLINLDVNNPDFKAGVMALA
CP.KIQ..QEAIDWLLGLA.RLEY.DN..KYKDL..DN..N.DNATKNAEPLIN..VNNP...AG..ALA
RetrocopyCPSKIQAQQEAIDWLLGLAIRLEYEDNTQKYKDLALDNT*NTDNATKNAEPLINSSVNNPNLNAGIKALA
ParentalNLLQIQRHDDYLVMLKAIRILVQE
NLLQIQ.HDDYLV..K.I.ILVQE
RetrocopyNLLQIQCHDDYLVIHKIIHILVQE

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 .00 RPM 39 .40 RPM
SRP017611_kidney 0 .00 RPM 97 .57 RPM
SRP017611_liver 0 .00 RPM 84 .09 RPM
SRP040447_lung 0 .00 RPM 61 .31 RPM
SRP040447_skeletal_muscle 0 .00 RPM 104 .77 RPM

ChIP-Seq - click to see more details

Cavia porcellus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cpor_1239 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_1239 was not experimentally validated.

Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 29 parental genes, and 70 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000020832 retrocopies
retro_amel_224, retro_amel_302,
Canis familiaris ENSCAFG000000146484 retrocopies
retro_cfam_1025, retro_cfam_2042, retro_cfam_237, retro_cfam_734,
Callithrix jacchus ENSCJAG000000069263 retrocopies
retro_cjac_1262, retro_cjac_1947, retro_cjac_3207,
Cavia porcellus ENSCPOG00000001317 6 retrocopies
retro_cpor_1041, retro_cpor_1177, retro_cpor_1239 , retro_cpor_1247, retro_cpor_517, retro_cpor_541,
Dasypus novemcinctus ENSDNOG000000032483 retrocopies
retro_dnov_458, retro_dnov_572, retro_dnov_609,
Dipodomys ordii ENSDORG000000123351 retrocopy
retro_dord_619,
Equus caballus ENSECAG000000126001 retrocopy
retro_ecab_483,
Erinaceus europaeus ENSEEUG000000155831 retrocopy
retro_eeur_366,
Felis catus ENSFCAG000000026633 retrocopies
retro_fcat_1160, retro_fcat_1415, retro_fcat_948,
Homo sapiens ENSG000000873021 retrocopy
retro_hsap_2307,
Loxodonta africana ENSLAFG000000031621 retrocopy
retro_lafr_301,
Microcebus murinus ENSMICG000000087201 retrocopy
retro_mmur_857,
Myotis lucifugus ENSMLUG000000086436 retrocopies
retro_mluc_1228, retro_mluc_1518, retro_mluc_1834, retro_mluc_2610, retro_mluc_456, retro_mluc_676,
Macaca mulatta ENSMMUG000000182002 retrocopies
retro_mmul_1045, retro_mmul_2025,
Monodelphis domestica ENSMODG000000132111 retrocopy
retro_mdom_1296,
Mustela putorius furoENSMPUG000000052536 retrocopies
retro_mputfur_1333, retro_mputfur_1421, retro_mputfur_203, retro_mputfur_328, retro_mputfur_655, retro_mputfur_797,
Mus musculus ENSMUSG000000218072 retrocopies
retro_mmus_140, retro_mmus_3203,
Nomascus leucogenys ENSNLEG000000124061 retrocopy
retro_nleu_2749,
Oryctolagus cuniculus ENSOCUG000000146811 retrocopy
retro_ocun_221,
Otolemur garnettii ENSOGAG000000132325 retrocopies
retro_ogar_1060, retro_ogar_1856, retro_ogar_2351, retro_ogar_2976, retro_ogar_3192,
Ochotona princeps ENSOPRG000000163522 retrocopies
retro_opri_257, retro_opri_884,
Pongo abelii ENSPPYG000000058141 retrocopy
retro_pabe_1980,
Pan troglodytes ENSPTRG000000063441 retrocopy
retro_ptro_1631,
Pteropus vampyrus ENSPVAG000000133921 retrocopy
retro_pvam_1088,
Sus scrofa ENSSSCG000000050291 retrocopy
retro_sscr_1093,
Tupaia belangeri ENSTBEG000000138985 retrocopies
retro_tbel_2579, retro_tbel_4337, retro_tbel_683, retro_tbel_880, retro_tbel_881,
Tarsius syrichta ENSTSYG000000045286 retrocopies
retro_tsyr_1183, retro_tsyr_1289, retro_tsyr_1353, retro_tsyr_157, retro_tsyr_541, retro_tsyr_939,
Tursiops truncatus ENSTTRG000000057211 retrocopy
retro_ttru_83,
Vicugna pacos ENSVPAG000000114431 retrocopy
retro_vpac_142,


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