RetrogeneDB ID:

retro_cpor_430

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_15:1208617..1209369(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPS15
Ensembl ID:ENSCPOG00000010877
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_430
ATGTCGAGGGCCACATGGAAGGCACTGAGTTCATTTGGATTCTGGGCAGCAAATCAAGCTCCAGTCTTTGGTCTTCTGGG
AAGAGGGAGTACTAGGCTTCTCTCAGATCAATGGGGCCTGCAGCCTCAAAATCCACAGACTGCTCAAAGATTTTCCACTC
AGAAACCAGTCCAACTCAGACACATCAATGATCTACCCTATTTCATGCTCTTCAGAGGCCACCAAAACATCCCTGCAATC
GAGAAAGGTGATGACATTGTGTAAAGACTCTTTGGATATGGTCAACTGGAAAGAAATGCAAAAATTAAGCAAGAACATTT
TATGAACAAGTTCATGGCAAACCCTGAAGACACCAGATCGCTGGAGACTTGAATTGTTGCCTGGACCATTAAGATGTGCA
ATTATGAAGAATACATGCAGAAACAACCAAAGAACAAAGTCCACAAATGCTATCTACTGATGCACATTGACCAGAGAAAG
ATGTCCAAAAATCTCTGGAAGACCAACTATAATATATTTGAGAAGATATTCAGGGAGCTGAGATCAAGTACACCTTAGGA
GGACTCTACTACCAAAAAGCCCACCACCACTTCTTGGCCAAGAAGTTCATGTACATCTAAGTTTTCCAGGAGGTACAAAA
GCTGAAGAAGCAAAAACCAACCTTAATATCTGCAAAAGCAGCCCAGAGAGAAGATGGCTATCAGAACACAGAGGCTCCTT
TCAAAGTTTATAAAGAGGCACTTGAGGAAAAC

ORF - retro_cpor_430 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.11 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMLKAAWRAVSLFGFRAATQAPVFGLPGRGRARLLSDQWGLQPQSLLQAACGYATQNPVQPCHDNDPPPST
M..A.W.A.S.FGF.AA.QAPVFGL.GRG..RLLSDQWGLQPQ...Q.A....TQ.PVQ..H.ND.P...
RetrocopyMSRATWKALSSFGFWAANQAPVFGLLGRGSTRLLSDQWGLQPQN-PQTAQRFSTQKPVQLRHINDLPYFM
ParentalLLKDYQNVPGIEKVDDVVKRLLSLEMANRKEMLKVKQEQLMNKVMANPEDTRALETRIVALTVKIRNYEE
L....QN.P.IEK.DD.V.RL.......R....K.KQE..MNK.MANPEDTR.LET.IVA.T.K..NYEE
RetrocopyLFRGHQNIPAIEKGDDIV*RLFGYGQLERN--AKIKQEHFMNKFMANPEDTRSLET*IVAWTIKMCNYEE
ParentalHMQKHRKDKAHKRYLLMSIDQRKKMLKNLRKTNYNIFERVCREL-GIEYTFPPLYYRKAHRRFLAKKALC
.MQK..K.K.HK.YLLM.IDQR.KM.KNL.KTNYNIFE...REL..I.YT...LYY.KAH..FLAKK...
RetrocopyYMQKQPKNKVHKCYLLMHIDQR-KMSKNLWKTNYNIFEKIFREL<EIKYTLGGLYYQKAHHHFLAKKFMY
ParentalIQVFQEVQKLKKQKRAL-KAKAALKQDDHQNEEAHSKAYAEALEEN
I.VFQEVQKLKKQK..L..AKAA...D..QN.EA..K.Y.EALEEN
RetrocopyI*VFQEVQKLKKQKPTLISAKAAQREDGYQNTEAPFKVYKEALEEN

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 .40 RPM 35 .66 RPM
SRP017611_kidney 0 .42 RPM 46 .59 RPM
SRP017611_liver 0 .57 RPM 35 .17 RPM
SRP040447_lung 0 .08 RPM 19 .04 RPM
SRP040447_skeletal_muscle 0 .03 RPM 64 .07 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_430 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_430 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 19 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000014631 retrocopy
Canis familiaris ENSCAFG000000303901 retrocopy
Callithrix jacchus ENSCJAG000000018523 retrocopies
Cavia porcellus ENSCPOG00000010877 1 retrocopy
retro_cpor_430 ,
Dipodomys ordii ENSDORG000000075811 retrocopy
Felis catus ENSFCAG000000052651 retrocopy
Homo sapiens ENSG000001168981 retrocopy
Myotis lucifugus ENSMLUG000000064751 retrocopy
Monodelphis domestica ENSMODG000000178131 retrocopy
Mus musculus ENSMUSG000000288611 retrocopy
Nomascus leucogenys ENSNLEG000000114671 retrocopy
Otolemur garnettii ENSOGAG000000026562 retrocopies
Pongo abelii ENSPPYG000000015371 retrocopy
Pan troglodytes ENSPTRG000000005411 retrocopy
Sus scrofa ENSSSCG000000263931 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000006081 retrocopy
Tupaia belangeri ENSTBEG000000009584 retrocopies
Tarsius syrichta ENSTSYG000000089482 retrocopies
Tursiops truncatus ENSTTRG000000023451 retrocopy



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