RetrogeneDB ID:

retro_cpor_1256

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_6:49773561..49774355(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EEF1A1
Ensembl ID:ENSCPOG00000004067
Aliases:None
Description:Elongation factor 1-alpha [Source:UniProtKB/TrEMBL;Acc:H0V2B3]


Retrocopy-Parental alignment summary:






>retro_cpor_1256
ATGGGAAAGGAAACGATTCTCATTGATATCCTTGTCATTGGATTCATAGATTCAAGCAAGTCCACTACTACTGGCCATCT
CATTGACAAATTTGGCGGCACTGACAAAGAACCACTAAAAACTCTGAGAGGCAGGCTGCTGAGATGGGGAAGATTCCTTC
AAATATGCCTGGGTCTTGGATAAATTGAAAGCCAAGTGTGAGTGTGGTAAACCCATTGACATCTCCCTGTGGAAATTTGA
GATGAGTAATTATTATGTGACTATCACTGATGCTCCTGGACACAGAGACTTTATCAAAAGCATGATTGCAGGCACATTTC
AGGCTGACTGTGCTGTTCTGATTGTTGCTGCCATTGTTGGTGAATTCAAAGCTGGTATCTCCAAGAACGGGCAGACCCAT
GATCATGCCCTTCTGGCTTACATGCTGGGTGTGAAACAACTAACTGTCAGTGTTAACTAAATGGATTCCACTGAGCTAAC
CTTCAGCCAGAAGAGATACAAGGAAATTGTTAAAAAATTCAGCACCTTCATTAAGCAAATTGGCTACAATCCTGACATGG
TGGGTTTTATGCTAATTTCTAGTTGGAATGGTGACAGTATGCTGGACCTAAGAGCTAATATGCCTCAGTTCAAGGGATGG
AAGGTCTCTCATAAAAATGACATTGCCTTTGGAACTACACTGCTTGAAGCTTTGGATTACATACTTGCACCAACTCACCC
AACTGACAAACTATGGGGCTGCCTCCCCAGGATGCCTCCAAAATTGGTGGTATTGGTACCATCCTGTGGGAAAA

ORF - retro_cpor_1256 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.85 %
Parental protein coverage: 57.58 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDK-RTIEKFEKEAAEMGK-GSFKYAWVLDKLKAERE
MGKE...I.I.VIG..DS.KSTTTGHLI.K.GG.DK.RT....E..AAEMGK..SFKYAWVLDKLKA..E
RetrocopyMGKETILIDILVIGFIDSSKSTTTGHLIDKFGGTDK<RTTKNSERQAAEMGK<DSFKYAWVLDKLKAKCE
ParentalRGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHAL
.G..IDISLWKFE.S.YYVTI.DAPGHRDFIK.MI.GT.QADCAVLIVAA.VGEF.AGISKNGQT..HAL
RetrocopyCGKPIDISLWKFEMSNYYVTITDAPGHRDFIKSMIAGTFQADCAVLIVAAIVGEFKAGISKNGQTHDHAL
ParentalLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANM
LAY.LGVKQL.V.VN.MDSTE...SQKRY.EIVK..ST.IK.IGYNPD.V.F..IS.WNGD.ML...ANM
RetrocopyLAYMLGVKQLTVSVN*MDSTELTFSQKRYKEIVKKFSTFIKQIGYNPDMVGFMLISSWNGDSMLDLRANM
ParentalPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDK-PLRLPLQDVYKIGGIGTV-PVGR
P.FKGWKV..K...A.GTTLLEALD.IL.PT.PTDK....LP.QD..KIGGIGT..PVG.
RetrocopyPQFKGWKVSHKNDIAFGTTLLEALDYILAPTHPTDK<TMGLPPQDASKIGGIGTI<PVGK

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 855 .04 RPM
SRP017611_kidney 0 .00 RPM 1991 .99 RPM
SRP017611_liver 0 .00 RPM 1852 .07 RPM
SRP040447_lung 0 .00 RPM 3418 .91 RPM
SRP040447_skeletal_muscle 0 .00 RPM 830 .52 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1256 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1256 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 15 parental genes, and 83 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000132491 retrocopy
Callithrix jacchus ENSCJAG000000100516 retrocopies
Cavia porcellus ENSCPOG00000004067 15 retrocopies
Dipodomys ordii ENSDORG000000096291 retrocopy
Equus caballus ENSECAG000000222601 retrocopy
Erinaceus europaeus ENSEEUG000000003423 retrocopies
Loxodonta africana ENSLAFG000000280811 retrocopy
Macaca mulatta ENSMMUG0000000485215 retrocopies
Monodelphis domestica ENSMODG000000185334 retrocopies
Mus musculus ENSMUSG0000003774215 retrocopies
Nomascus leucogenys ENSNLEG000000014766 retrocopies
Pan troglodytes ENSPTRG000000183471 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000076874 retrocopies
Vicugna pacos ENSVPAG000000076379 retrocopies
Drosophila melanogaster FBgn00005571 retrocopy



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