RetrogeneDB ID:

retro_itri_1567

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393544.1:1632977..1633581(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000024672
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPA1L2
Ensembl ID:ENSSTOG00000006551
Aliases:None
Description:heterogeneous nuclear ribonucleoprotein A1-like 2 [Source:HGNC Symbol;Acc:27067]


Retrocopy-Parental alignment summary:






>retro_itri_1567
ATGTCTAAATCAGAGTCCCCTAAAGAGCCCGAACAGCTGCAGAAGCTATTCATCGGAGGGCTGAGCTTTGAAACAACTGA
TGAGAGTCTAAGAAGCCATTTTGAGCAATGGGGAACACTCACGGATTGTGTGGTAACGAGAGATCCAAACACCAAGCGCT
CCAGAGGCTTTGGGTTTGTCACTTATGCCACTGTGGAGGAAGTGGATGCAGCCATGAATGCAAGACCACACAAAGTGGAT
GGCAGAGTTGTAGAACCAAAGAGATCTGTCTCATGAGAAATTCTCAAAGACTAGGGGCCCACTTAACTGTGAAAAAGATC
TTTGTTGGTGGCATTAAAGAAGACACTAAAGAATATCTCCTACGAGATTATTTTGAACAGTATGGGAAAACTGAAGTTAT
TGAAATCATGACTGACCGAAGCAGTGGAAAGAAAAGGGGCTTTGCTTTTGTAACTTTTGATGACCATGACTCTGTGGATA
AGATTGTCATTCAGAAATACATACTGTGAATGGCCACAAATGTGAAGTGAGGAAAGCCCTGACAAAGCAAGAGATGGCTA
GTGCCTCATCTAGCCAAAGAGGTCAAAGCGGTTCTGGAAACTTC

ORF - retro_itri_1567 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.16 %
Parental protein coverage: 54.01 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA
MSKSESPKEPEQL.KLFIGGLSFETTDESLRSHFEQWGTLTDCVV.RDPNTKRSRGFGFVTYATVEEVDA
RetrocopyMSKSESPKEPEQLQKLFIGGLSFETTDESLRSHFEQWGTLTDCVVTRDPNTKRSRGFGFVTYATVEEVDA
ParentalAMNARPHKVDGRVVEPKRAVSRE-DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD
AMNARPHKVDGRVVEPKR.VS.E..SQR.GAHLTVKKIFVGGIKEDT.E..LRDYFEQYGK.EVIEIMTD
RetrocopyAMNARPHKVDGRVVEPKRSVS*E<NSQRLGAHLTVKKIFVGGIKEDTKEYLLRDYFEQYGKTEVIEIMTD
ParentalRGSGKKRGFAFVTFDDHDSVDKIVIQKY-HTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNF
R.SGKKRGFAFVTFDDHDSVDKIVIQKY.HTVNGH.CEVRKAL.KQEMASASSSQRG.SGSGNF
RetrocopyRSSGKKRGFAFVTFDDHDSVDKIVIQKY<HTVNGHKCEVRKALTKQEMASASSSQRGQSGSGNF

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