RetrogeneDB ID:

retro_cpor_981

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_38:10566689..10567888(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000020752
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ARPC1A
Ensembl ID:ENSCPOG00000001777
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_981
ACTGACCAGAGTCAGCGAATTCTCCGCTGCGAGCCCCTTCAGACCGCCCAGACCTCAAGAGCAGCATTGCTTTCTATCCT
TTGAAAACACTAAGAATATGTCCCTGCATCAGTTTTTACTAGAGCCAATCACCTGTCATGCCTGGAACAGAGACCATACC
CGAATTGCCCTTAGCCCCAGTAATCACGAAGTTCACATCTATAAGAATGGGAGCCAGTGGGTGAAAGCTCATGAACTCAA
GGAGCACAACGAATCACAGGGATTGACTGGGCTCCCAAGAGCGATCGCATTGTCACTTGTGGAGCCGACCGCAATGCCTA
CGTCTGGAATCAGAAAGATAGTGTCTGGAAGCCAACCTTGGTGATCCTGAGGATTAACCGCGCAGCCACTTTTGTGAAGT
GGTCCCCTCTAGCGAACAAATTTGCTGTGGGAAGTGGAGCACGACTCATTTCTGTTTGTTACTTTGAATCTGAAAATGAC
TGGTGGGTAAGCAAGCACATTAAAAAGCCGATTCGCTCTACAGTCCTCAGCTTGGATTGGCATCCCAACAATGTTTTACT
TGCAGCAGGATCCTGTGATTTCAAGTGCAGAGTGTTTTCTGCCTACATTAAAGAAGTGGATGAAAAGCCAGCCAGTACAC
CCTGGGGCAGCAAGATGCCTTTTGGCCAACTGATGTCAGAGTTTGTGGCAGTGGCACTGGTGGCTGGGTCCATGGAGTCA
GCTTCTCTGCCAGTGGGAGTCGTCTGGCTTGGGTCAGCCATGACAGTACTGTGTCTGTTGCTGATGTCTCAAAAAGTGTA
CAGGTCTCCACTCTGAAAACCGAGTTCCTGCCACTCCTGAGTGTGTCGTTTGTCTCTGAGAACAGTGTTGTGGCTGCTGG
CCATGACTGTTGTCTGATGCTCTTTAACTATGATGACCGCGGCTGCTTGACCTTTGTCTCCAAGCTTGACATTCCAAAAC
AGAGCATCCAGCACGACATGTCTGCCATGGAATGCTTCCGCAACATGGACAAAAGGGCGACAACTGAGGACCGTAATACC
GCTTTGGAGACACTGCACCAGAATAGCATCACTCAAGTGTCTATTTATGAGGTGGACAAGCAAGATTGTCGCAAATTTTG
CGCTACTGGCATCAATGGAGCCATGACAATTTGGGACTTCAAGACCTTCGAGTCTTCGATCCAAGGCCTCTGAATAATG

ORF - retro_cpor_981 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.12 %
Parental protein coverage: 99.5 %
Number of stop codons detected: 1
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalTDQSPRILRCE-PLQTAQTSIYCSFLSFENTKNMSLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYKK
TDQS.RILRCE.P...........FLSFENTKNMSLHQFLLEPITCHAWNRD.T.IALSP.NHEVHIY.K
RetrocopyTDQSQRILRCE>PFRPPRPQEQHCFLSFENTKNMSLHQFLLEPITCHAWNRDHTRIALSPSNHEVHIY-K
ParentalNGSQWVKAHELKEHNGHITGIDWAP-KSDRIVTCGADRNAYVWSQKDGVWKPTLVILRINRAATFVKWSP
NGSQWVKAHELKEHN....G....P.KSDRIVTCGADRNAYVW.QKD.VWKPTLVILRINRAATFVKWSP
RetrocopyNGSQWVKAHELKEHN-ESQGLTGLP<KSDRIVTCGADRNAYVWNQKDSVWKPTLVILRINRAATFVKWSP
ParentalLENKFAVGSGARLISVCYFESENDWWVSKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEV
L.NKFAVGSGARLISVCYFESENDWWVSKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEV
RetrocopyLANKFAVGSGARLISVCYFESENDWWVSKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEV
ParentalDEKPASTPWGSKMPFGQLMSEF-GGSGTGGWVHGVSFSASGSRLAWVSHDSTVSVADASKSVQVSTLKTE
DEKPASTPWGSKMPFGQLMSEF..GSGTGGWVHGVSFSASGSRLAWVSHDSTVSVAD.SKSVQVSTLKTE
RetrocopyDEKPASTPWGSKMPFGQLMSEF<CGSGTGGWVHGVSFSASGSRLAWVSHDSTVSVADVSKSVQVSTLKTE
ParentalFLPLLSVSFVSENSVVAAGHDCCPMLFNYDDRGCLTFVSKLDIPKQSIQRNMSAMERFRNMDKRATTEDR
FLPLLSVSFVSENSVVAAGHDCC.MLFNYDDRGCLTFVSKLDIPKQSIQ..MSAME.FRNMDKRATTEDR
RetrocopyFLPLLSVSFVSENSVVAAGHDCCLMLFNYDDRGCLTFVSKLDIPKQSIQHDMSAMECFRNMDKRATTEDR
ParentalNTALETLHQNSITQVSIYEVDKQDCRKFCTTGIDGAMTIWDFKTLESSIQGLRIM
NTALETLHQNSITQVSIYEVDKQDCRKFC.TGI.GAMTIWDFKT.ESSIQGL.IM
RetrocopyNTALETLHQNSITQVSIYEVDKQDCRKFCATGINGAMTIWDFKTFESSIQGL*IM

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 .12 RPM 32 .61 RPM
SRP017611_kidney 0 .00 RPM 43 .55 RPM
SRP017611_liver 0 .00 RPM 17 .06 RPM
SRP040447_lung 0 .00 RPM 57 .63 RPM
SRP040447_skeletal_muscle 0 .01 RPM 22 .14 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_981 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_981 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 21 parental genes, and 54 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063221 retrocopy
retro_amel_1431,
Bos taurus ENSBTAG000000042421 retrocopy
retro_btau_1486,
Callithrix jacchus ENSCJAG000000158593 retrocopies
retro_cjac_2141, retro_cjac_2165, retro_cjac_2263,
Cavia porcellus ENSCPOG00000001777 2 retrocopies
retro_cpor_452, retro_cpor_981 ,
Dipodomys ordii ENSDORG000000160591 retrocopy
retro_dord_593,
Equus caballus ENSECAG000000164671 retrocopy
retro_ecab_185,
Homo sapiens ENSG000002416852 retrocopies
retro_hsap_2010, retro_hsap_3191,
Loxodonta africana ENSLAFG000000140241 retrocopy
retro_lafr_1006,
Macropus eugenii ENSMEUG000000056098 retrocopies
retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Myotis lucifugus ENSMLUG000000109121 retrocopy
retro_mluc_1432,
Macaca mulatta ENSMMUG000000193422 retrocopies
retro_mmul_1383, retro_mmul_2012,
Monodelphis domestica ENSMODG000000013039 retrocopies
retro_mdom_1360, retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917, retro_mdom_686, retro_mdom_699, retro_mdom_808,
Mus musculus ENSMUSG000000296211 retrocopy
retro_mmus_1373,
Nomascus leucogenys ENSNLEG000000108522 retrocopies
retro_nleu_1663, retro_nleu_2069,
Oryctolagus cuniculus ENSOCUG000000039441 retrocopy
retro_ocun_1130,
Otolemur garnettii ENSOGAG000000108706 retrocopies
retro_ogar_1547, retro_ogar_2690, retro_ogar_2697, retro_ogar_381, retro_ogar_610, retro_ogar_656,
Pongo abelii ENSPPYG000000258164 retrocopies
retro_pabe_1647, retro_pabe_1648, retro_pabe_2537, retro_pabe_2647,
Pan troglodytes ENSPTRG000000338192 retrocopies
retro_ptro_1340, retro_ptro_2253,
Sarcophilus harrisii ENSSHAG000000106732 retrocopies
retro_shar_180, retro_shar_727,
Ictidomys tridecemlineatus ENSSTOG000000016601 retrocopy
retro_itri_1834,
Tupaia belangeri ENSTBEG000000113813 retrocopies
retro_tbel_1237, retro_tbel_1241, retro_tbel_82,


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