RetrogeneDB ID:

retro_sscr_1025

Retrocopy
location
Organism:Pig (Sus scrofa)
Coordinates:9:49470252..49470717(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSSCG00000023219
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSSCG00000017768
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_sscr_1025
ATGGGGCAGAAGGCGAAGAAGGAAGCCCCTGGCCCTCCCAAAGCCGAAGCCAAAGCAAAGGCTTTGAAGGCCAAGAAAGC
AGTGTTGAAAGGCGTCCACAGCCACAAAAAAAAGAAGATCCAGATGTCACCGACCTCCTGATGGCCCAAAACACTACGAC
TCAGGAGGCAGCCCAAATATCCTCAGAGGAGCACCCCTAGGAGAAACAATCTTGACCACTATGCCATCATCAAGCTCCCC
CTCACCACTGAGTCGGCCATGAAGAAGATAGAGGACAACAACACACTTGTGTTCATTGTGGATGTCAAGGCCAACAAGCA
CCAGATTAAACAGGCTGTGAAGAACCTCTATGACACTGATGTGGCTAAGGTCAACACTCTGATCAGGCCTGATGGAGAGA
AGGCATATGTTCAACTAGCTTCTGACTATGATGCTTTGGATGTTACTAACAAAATTGGGATTATC

ORF - retro_sscr_1025 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.9 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAPKAKKEAPAPPKAEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNK
M..KAKKEAP.PPKAEAKAKALKAKKAVLKGVHSH...KI..SPT...PKTLRLRRQPKYP..S.PRRN.
RetrocopyMGQKAKKEAPGPPKAEAKAKALKAKKAVLKGVHSHXXXKIQMSPTS*WPKTLRLRRQPKYPQRSTPRRNN
ParentalLDHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRL
LDHYAIIK.PLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVK.LYD.DVAKVNTLIRPDGE.KAYV.L
RetrocopyLDHYAIIKLPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKNLYDTDVAKVNTLIRPDGE-KAYVQL
ParentalAPDYDALDVANKIGII
A.DYDALDV.NKIGII
RetrocopyASDYDALDVTNKIGII

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 .13 RPM 1 .06 RPM
SRP014902_testis 0 .00 RPM 10 .18 RPM
SRP018288_heart 0 .03 RPM 1 .05 RPM
SRP018288_kidney 0 .00 RPM 0 .99 RPM
SRP018288_liver 0 .16 RPM 1 .92 RPM
SRP018288_lung 0 .10 RPM 2 .75 RPM
SRP018856_adipose 0 .03 RPM 1 .23 RPM
SRP035408_brain 0 .48 RPM 0 .76 RPM
SRP035408_liver 0 .41 RPM 0 .56 RPM
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1025 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1025 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_sscr_1025 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 21 parental genes, and 467 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000053112 retrocopies
Bos taurus ENSBTAG000000463946 retrocopies
Callithrix jacchus ENSCJAG000000131267 retrocopies
Dasypus novemcinctus ENSDNOG0000001948765 retrocopies
Felis catus ENSFCAG0000000402135 retrocopies
Homo sapiens ENSG0000019824257 retrocopies
Gorilla gorilla ENSGGOG0000001673626 retrocopies
Loxodonta africana ENSLAFG0000001338716 retrocopies
Myotis lucifugus ENSMLUG000000124484 retrocopies
Monodelphis domestica ENSMODG000000192973 retrocopies
Mustela putorius furoENSMPUG0000001417912 retrocopies
Mus musculus ENSMUSG000000585468 retrocopies
Nomascus leucogenys ENSNLEG0000000287260 retrocopies
Procavia capensis ENSPCAG0000001700230 retrocopies
Pongo abelii ENSPPYG0000000810849 retrocopies
Pteropus vampyrus ENSPVAG0000000292232 retrocopies
Rattus norvegicus ENSRNOG000000233446 retrocopies
Sarcophilus harrisii ENSSHAG0000001454913 retrocopies
Sus scrofa ENSSSCG00000017768 9 retrocopies
Sus scrofa ENSSSCG000000298024 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000001132823 retrocopies



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