RetrogeneDB ID:

retro_cpor_1510

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_91:308090..308653(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL12
Ensembl ID:ENSCPOG00000013769
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_1510
CAACTTTTGGCTAGCAGTAGGCTAAGCTGCAACTTTCTTGAGTCAACCTGTATCTGGCTTTTTCTGACACCAGCTACTTC
CAACATACTGCCTACAGTTCAACACAGTGAGATCAAAGTCATGTACCTGAAGTGCTCTGTGGTGAAGTCAGTGTCCACAT
CTGCTCTGGCCTCAAGACTGGCCTCTTAGGTCTGTGTCCAAAAATAGTGGGAGATGACATTACAGAGGCAGCAAATGATT
GGTAGGATTTGAGGGTTATGTTGAAATTGAATATTCAGAACACAAAGGCCCAGATTGAGGTAGTGCCTTCTGCCCCTGCC
CTGATCATCAGAGTCCCCAAATATCTGACAAGAAACAGAAAAATATTAAACACAAGAGAAATATCACTTTTGACAAGACT
CAACAATGCCCAACAGATGTGGCACTGGTCTTTAGCCAGAGAACTTTCTGGAAGTAATACAGAGGTCCTGAGGACCACCC
AGCCTGTGAGCTGCCATGTGGGTAGCAAATACCCCCATAAAATTATAGAGGACATCAACAATGGTGCTGTGGAGTGTCCA
GCT

ORF - retro_cpor_1510 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 51.81 %
Parental protein coverage: 98.46 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRLSARRRQRCNFLRSSRIRVHPTPAASTMPPKFDPNEIKVVYLRCTGGEVGATSALAPKI-GPLGLSPKK
.L.A..R..CNFL.S..I....TPA.S...P.....EIKV.YL.C.......TSALA....G.LGL.PK.
RetrocopyQLLASSRLSCNFLESTCIWLFLTPATSNILPTVQHSEIKVMYLKCSVVKSVSTSALASRL<GLLGLCPKI
ParentalVGDDIAKATGDWKGLRITVKLTIQNRQAQIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVN
VGDDI..A..DW..LR...KL.IQN..AQIEVVPSA.ALII...K...R.RK....I.....I......N
RetrocopyVGDDITEAANDW*DLRVMLKLNIQNTKAQIEVVPSAPALIIRVPKYLTRNRK----ILNTREISLLTRLN
ParentalIARQMRHRSLARELSGTIKEILGTAQSVGCNVDNRHPHDIIDDINSGAVECPA
.A.QM.H.SLARELSG...E.L.T.Q.V.C.V....PH.II.DIN.GAVECPA
RetrocopyNAQQMWHWSLARELSGSNTEVLRTTQPVSCHVGSKYPHKIIEDINNGAVECPA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 83 .11 RPM
SRP017611_kidney 0 .00 RPM 202 .78 RPM
SRP017611_liver 0 .00 RPM 146 .95 RPM
SRP040447_lung 0 .00 RPM 273 .72 RPM
SRP040447_skeletal_muscle 0 .00 RPM 242 .39 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1510 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1510 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 16 parental genes, and 319 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001671215 retrocopies
Canis familiaris ENSCAFG0000002013631 retrocopies
Cavia porcellus ENSCPOG00000013769 18 retrocopies
Equus caballus ENSECAG0000001062217 retrocopies
Echinops telfairi ENSETEG000000069417 retrocopies
Felis catus ENSFCAG0000001030231 retrocopies
Latimeria chalumnae ENSLACG000000153733 retrocopies
Macropus eugenii ENSMEUG0000000738012 retrocopies
Myotis lucifugus ENSMLUG000000095512 retrocopies
Myotis lucifugus ENSMLUG000000134041 retrocopy
Monodelphis domestica ENSMODG000000045719 retrocopies
Mustela putorius furoENSMPUG0000001383234 retrocopies
Otolemur garnettii ENSOGAG00000000597120 retrocopies
retro_ogar_1002, retro_ogar_1010, retro_ogar_1049, retro_ogar_1069, retro_ogar_1106, retro_ogar_1117, retro_ogar_1137, retro_ogar_1140, retro_ogar_1181, retro_ogar_1188, retro_ogar_1189, retro_ogar_1192, retro_ogar_1230, retro_ogar_1247, retro_ogar_1263, retro_ogar_1295, retro_ogar_1331, retro_ogar_1341, retro_ogar_1408, retro_ogar_1409, retro_ogar_1427, retro_ogar_1457, retro_ogar_1464, retro_ogar_1489, retro_ogar_1503, retro_ogar_1534, retro_ogar_1536, retro_ogar_1550, retro_ogar_1569, retro_ogar_1570, retro_ogar_1579, retro_ogar_1606, retro_ogar_1621, retro_ogar_1709, retro_ogar_1717, retro_ogar_1739, retro_ogar_1789, retro_ogar_1803, retro_ogar_1810, retro_ogar_1825, retro_ogar_1836, retro_ogar_1881, retro_ogar_1885, retro_ogar_1916, retro_ogar_1923, retro_ogar_1937, retro_ogar_1941, retro_ogar_1948, retro_ogar_1969, retro_ogar_1975, retro_ogar_1987, retro_ogar_2055, retro_ogar_2115, retro_ogar_2134, retro_ogar_2172, retro_ogar_2179, retro_ogar_2180, retro_ogar_2208, retro_ogar_2209, retro_ogar_2230, retro_ogar_2291, retro_ogar_2323, retro_ogar_2387, retro_ogar_2483, retro_ogar_2495, retro_ogar_2511, retro_ogar_2570, retro_ogar_2620, retro_ogar_2622, retro_ogar_2624, retro_ogar_2749, retro_ogar_2768, retro_ogar_2809, retro_ogar_2904, retro_ogar_2935, retro_ogar_2945, retro_ogar_2953, retro_ogar_2980, retro_ogar_3004, retro_ogar_3017, retro_ogar_303, retro_ogar_3035, retro_ogar_3128, retro_ogar_3135, retro_ogar_3164, retro_ogar_3394, retro_ogar_3489, retro_ogar_395, retro_ogar_398, retro_ogar_412, retro_ogar_427, retro_ogar_452, retro_ogar_480, retro_ogar_512, retro_ogar_513, retro_ogar_538, retro_ogar_560, retro_ogar_587, retro_ogar_624, retro_ogar_636, retro_ogar_653, retro_ogar_655, retro_ogar_667, retro_ogar_668, retro_ogar_669, retro_ogar_683, retro_ogar_700, retro_ogar_734, retro_ogar_737, retro_ogar_744, retro_ogar_747, retro_ogar_775, retro_ogar_818, retro_ogar_853, retro_ogar_868, retro_ogar_901, retro_ogar_927, retro_ogar_956, retro_ogar_962, retro_ogar_964,
Rattus norvegicus ENSRNOG000000162204 retrocopies
Sarcophilus harrisii ENSSHAG000000178648 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000274257 retrocopies



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