RetrogeneDB ID:

retro_sscr_898

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:7:31265834..31266291(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FTL
Ensembl ID:ENSSSCG00000003153
Aliases:None
Description:Sus scrofa ferritin, light polypeptide (FTL), mRNA. [Source:RefSeq mRNA;Acc:NM_001244131]


Retrocopy-Parental alignment summary:






>retro_sscr_898
TCGATGCATCTGAGGGCCTCCCACACCTACCTCTCCCTGCGTCTCTATTTCAACAGCAATGATGTGGCTCTGGAGAGCGT
GAGCCACTTTTTCTGCAAATTGGCTGAGGAGAAGCTGGAGGGCGCAGAGCGTCTCTTGAAAATGTAAAACTAGCGCAGTG
GTAGCGCCCTCTTCCAGAACATGAGAAGCCATCTCAAGAAGAGTCGGGTAAAACCAGGACGCTATGGAAGCTGCCATTCT
CTTGGAGAAGAACCTGAACCAGGCTCTTCTAGATCCGCATGCCCTGGGTTCTGCCCGTGCGGACCCGCATCTCTGTGACT
TCCTGGAGAGCCGATTCTTGGATGAGCAGGTGAAGCCCATCAAGACGATGGGAGACCACCTGTCCGACCTCCGTGGACTG
TCTGGTCCCCAGACTGGGCTGGGCGAGTACCTCTTTGAAAGTCTCACCCTCAAGCAC

ORF - retro_sscr_898 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.48 %
Parental protein coverage: 87.43 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalNMHLQASYTYLSLGFYFNRDDVALEGVSHFFRELAEEKREGSERLLKMQNQRGGRALFQDV-QKPSQDEW
.MHL.AS.TYLSL..YFN..DVALE.VSHFF..LAEEK.EG.ERLLKM.N.R.G.ALFQ....KPSQ.E.
RetrocopySMHLRASHTYLSLRLYFNSNDVALESVSHFFCKLAEEKLEGAERLLKM*N*RSGSALFQNM<EKPSQEES
ParentalGKT-QDAMEAALHLEKGLNQALVDLHALGSARADPHLCDFLENHFLDEEVKLIKKMGDHLTNLRRLSGPQ
GKT.QDAMEAA..LEK.LNQAL.D.HALGSARADPHLCDFLE..FLDE.VK.IK.MGDHL..LR.LSGPQ
RetrocopyGKT<QDAMEAAILLEKNLNQALLDPHALGSARADPHLCDFLESRFLDEQVKPIKTMGDHLSDLRGLSGPQ
ParentalAGLGEYLFERLTLKH
.GLGEYLFE.LTLKH
RetrocopyTGLGEYLFESLTLKH

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
SRP014902_placenta 0 .00 RPM 0 .00 RPM
SRP014902_testis 0 .00 RPM 0 .00 RPM
SRP018288_heart 0 .00 RPM 0 .00 RPM
SRP018288_kidney 0 .00 RPM 0 .00 RPM
SRP018288_liver 0 .00 RPM 0 .00 RPM
SRP018288_lung 0 .00 RPM 0 .00 RPM
SRP018856_adipose 0 .00 RPM 0 .00 RPM
SRP035408_brain 0 .00 RPM 0 .00 RPM
SRP035408_liver 0 .00 RPM 0 .00 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_898 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_898 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_898 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 34 parental genes, and 473 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001458227 retrocopies
Bos taurus ENSBTAG0000001334333 retrocopies
Canis familiaris ENSCAFG000000038611 retrocopy
Callithrix jacchus ENSCJAG0000000025013 retrocopies
Cavia porcellus ENSCPOG000000205581 retrocopy
Dasypus novemcinctus ENSDNOG000000024559 retrocopies
Dasypus novemcinctus ENSDNOG000000041265 retrocopies
Dasypus novemcinctus ENSDNOG0000000557736 retrocopies
Dasypus novemcinctus ENSDNOG000000078482 retrocopies
Dasypus novemcinctus ENSDNOG000000166838 retrocopies
Dipodomys ordii ENSDORG000000155505 retrocopies
Felis catus ENSFCAG0000000334837 retrocopies
Homo sapiens ENSG0000008708611 retrocopies
Gorilla gorilla ENSGGOG000000119999 retrocopies
Loxodonta africana ENSLAFG0000003124811 retrocopies
Microcebus murinus ENSMICG000000018617 retrocopies
Macaca mulatta ENSMMUG000000039099 retrocopies
Mustela putorius furoENSMPUG0000000330429 retrocopies
Mus musculus ENSMUSG000000507081 retrocopy
Nomascus leucogenys ENSNLEG0000000471610 retrocopies
Oryctolagus cuniculus ENSOCUG000000000146 retrocopies
Ochotona princeps ENSOPRG0000000249210 retrocopies
Procavia capensis ENSPCAG000000132276 retrocopies
Pongo abelii ENSPPYG0000001022311 retrocopies
Pan troglodytes ENSPTRG0000001126811 retrocopies
Pteropus vampyrus ENSPVAG0000000957025 retrocopies
Rattus norvegicus ENSRNOG000000208437 retrocopies
Sorex araneus ENSSARG0000001174112 retrocopies
Sus scrofa ENSSSCG00000003153 33 retrocopies
Sus scrofa ENSSSCG000000145409 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000206397 retrocopies
Tupaia belangeri ENSTBEG0000000531113 retrocopies
Tarsius syrichta ENSTSYG0000001398856 retrocopies
Vicugna pacos ENSVPAG000000055093 retrocopies



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