RetrogeneDB ID:

retro_cpor_88

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_19:7993720..7994908(+)
Located in intron of:ENSCPOG00000005593
Retrocopy
information
Ensembl ID:ENSCPOG00000000861
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:DDI2
Ensembl ID:ENSCPOG00000020885
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_88
ATGCTGATCACTGTGTACTGTGTACGGAGGGACCTCTCTGAGGAAACTTTCTCCCTTCAAGTCAGCCCTGACTTTGAGCT
CTGCAATTTCAAGGTCCTCTGTGAACTGGAGTCCAGAGTTCCTGCTGAAGAGATCCAGATTGTCTACATGGAGCGATTCC
TCACAGACAATCACTGTTCCTTGGGATCCTACGGCCTCAAAGATGGTGATGTTGTTGTTTTACTTCAGAGGGATAACGTG
GGATCTCGGCCTCCAGGACAAACCCCAAACCAGTCTCGAGTTGATTTCAGTACAGTTCCTCAGCCTGGAACATCAAGCTC
TCGACAGCAGCACCAGCACCAACACCAGCACCAGCAGCAGAATCACCAGCAGCAGAAGCACAAACATGCTTCCTCAGCCC
AGCGGTCCCATGGCTTGGCTTCTGGAGAGAAGAGGGCCTCTGCCGCGGGTATGGACAGTCCTGCTGCGATTCGCAGTATG
TTGCTTTCCAGTCCCCATGATCTGTCTTTGCTGAAGGAACGCAACCCTGTTTTAGCTGAAGCTCTCCTCAGTGGAAACCT
TGAGACATTTTCTCGGGTTCTGATGGAACAGCAAAGAGAAATAGCCTTGAGGGAAGAAGAGAGGCTACGCCTCTTTTCTG
CTGATCCATTTGATCAAGAAGCTCAGGCTAAAATAGAAGAAGAAATTCGGCAGCAGAACATTGAAGAAAACATGAACATA
GCTATGGAGGAGGCTCCTGAGAGTTTTGGACAGGTGACGATGCTCTATATAAACTGCAAAGTGAATGGGTATCCTCTGAA
GGCTTTTGTTGACTCAGGTGCCCAGATGACCATTATGAGCCAAGCTTGTGCTGAGAGGTGTAACATAATTAGGCTGGTGG
ACCGACGGTGGGCTGGAGTTGCTAAAGGAGTGGGCACACAGAGGATTATTGGTCGTGTTCATCTAGCTCAGATTCAAATT
GAAGGTGATTTCTTACAATGCTCCTTCTCTGTGCTTGAGGAGCAACCCATGGATATCCTCCTAGGACTAGATATGCTTAG
GAGACATCAATGTTCCATTGATTTGAAGAAAAATGTGCTGGTTATTGGCACCACTGGCACACAGACTTACTTTCTCCCAG
AGGGTGAGTTACCCTTATGTGCTAAACTAGTAAGTGGTATTGGGCAGGAAGATCCTTCCAACAAAGAA

ORF - retro_cpor_88 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.29 %
Parental protein coverage: 73.91 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRQRPAAGAQQPHSSA-GEIASSPQGLDNPALLRDMLLANPHELSLLKERNPPLAEALLSGDLERFSRVLV
....A..AQ..H..A.GE...S..G.D.PA..R.MLL..PH.LSLLKERNP.LAEALLSG.LE.FSRVL.
RetrocopyKHKHASSAQRSHGLASGEKRASAAGMDSPAAIRSMLLSSPHDLSLLKERNPVLAEALLSGNLETFSRVLM
ParentalEQQQDRARREQERIRLFSADPFDLEAQAKIEEDIRQQNIEENMTIAMEEAPESFGQVVMLYINCKVNGHP
EQQ...A.RE.ER.RLFSADPFD.EAQAKIEE.IRQQNIEENM.IAMEEAPESFGQV.MLYINCKVNG.P
RetrocopyEQQREIALREEERLRLFSADPFDQEAQAKIEEEIRQQNIEENMNIAMEEAPESFGQVTMLYINCKVNGYP
ParentalVKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGIAKGVGTQKIIGRVHLALAQVQIEGDFLACSFSILE
.KAFVDSGAQMTIMSQACAERCNI.RLVDRRWAG.AKGVGTQ.IIGRVH..LAQ.QIEGDFL.CSFS.LE
RetrocopyLKAFVDSGAQMTIMSQACAERCNIIRLVDRRWAGVAKGVGTQRIIGRVH--LAQIQIEGDFLQCSFSVLE
ParentalEQPMDMLLGLDMLKRHQCSIDLKKNVLVIGTTGSQTSFLPEGELPECARLAYGTGREDVRPEE
EQPMD.LLGLDML.RHQCSIDLKKNVLVIGTTG.QT.FLPEGELP.CA.L..G.G.ED....E
RetrocopyEQPMDILLGLDMLRRHQCSIDLKKNVLVIGTTGTQTYFLPEGELPLCAKLVSGIGQEDPSNKE

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 4 .08 RPM
SRP017611_kidney 0 .10 RPM 6 .80 RPM
SRP017611_liver 0 .00 RPM 14 .41 RPM
SRP040447_lung 0 .03 RPM 5 .37 RPM
SRP040447_skeletal_muscle 0 .01 RPM 3 .53 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_88 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_88 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 24 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000118731 retrocopy
retro_amel_10,
Bos taurus ENSBTAG000000187182 retrocopies
retro_btau_15, retro_btau_650,
Canis familiaris ENSCAFG000000162201 retrocopy
retro_cfam_193,
Callithrix jacchus ENSCJAG000000086251 retrocopy
retro_cjac_196,
Cavia porcellus ENSCPOG00000020885 1 retrocopy
retro_cpor_88 ,
Equus caballus ENSECAG000000007621 retrocopy
retro_ecab_110,
Homo sapiens ENSG000001973121 retrocopy
retro_hsap_96,
Gorilla gorilla ENSGGOG000000135371 retrocopy
retro_ggor_143,
Macropus eugenii ENSMEUG000000061481 retrocopy
retro_meug_1364,
Myotis lucifugus ENSMLUG000000306691 retrocopy
retro_mluc_68,
Macaca mulatta ENSMMUG000000199121 retrocopy
retro_mmul_231,
Monodelphis domestica ENSMODG000000035151 retrocopy
retro_mdom_282,
Mustela putorius furoENSMPUG000000163321 retrocopy
retro_mputfur_1509,
Mus musculus ENSMUSG000000785151 retrocopy
retro_mmus_67,
Oryctolagus cuniculus ENSOCUG000000238911 retrocopy
retro_ocun_249,
Otolemur garnettii ENSOGAG000000277091 retrocopy
retro_ogar_4,
Ochotona princeps ENSOPRG000000184481 retrocopy
retro_opri_4,
Pongo abelii ENSPPYG000000018411 retrocopy
retro_pabe_158,
Pan troglodytes ENSPTRG000000240591 retrocopy
retro_ptro_570,
Pteropus vampyrus ENSPVAG000000050841 retrocopy
retro_pvam_420,
Rattus norvegicus ENSRNOG000000122741 retrocopy
retro_rnor_2606,
Sus scrofa ENSSSCG000000034621 retrocopy
retro_sscr_6,
Ictidomys tridecemlineatus ENSSTOG000000194471 retrocopy
retro_itri_93,
Tarsius syrichta ENSTSYG000000025221 retrocopy
retro_tsyr_1120,




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