RetrogeneDB ID:

retro_itri_48

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393491.1:1822742..1823855(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000019472
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSTOG00000016395
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_itri_48
ATGGATGTAGAAGCCAAGTACCGCATGGCCTCCTTGTACGTGGGTGACCTGCACGTAGATGTCACCGAGGACCTATTGTT
CAGGAAGTTCAGTGCGGTGGGCCCTGTGCTGTCCATCCGCATCTGCAGGGACGCGGTCACCCGCCTCTCTCTGGGCTATG
CTTACGTGAACTTCCTGCAGTTGGCCGATGCCCAGAAGGCTCTAGACACCATGAACTTTGACACGATAAAAGGCAAATCC
ATCCGTCTCATGTGGTCTCAAAGGGATGCCCACCTAAGGAAATCTGGAGTTGGGAATGTGTTCATCAAAAACCTGGACAA
ATCCATAGATAACAAGACGCTGCACGAACATTTTTCAGCTTTTGGAAAGATCCTTTCCTCCAAGGTGATGAGTGATGACC
AAGGCTCCAAGGGTTACGGCTTCGTGCACTTTCAGAACCAGAGCGCGGCCGAGAAGGCCATCGAGGAGATGAACGGGAAG
CTGCTCAAAGACTGCAGGGTGTTTGTGGGCAGATTCAAAAACCGCAAGGAGCGCGAGGCCGAGCTCAGAAGCAAAGCCTC
CAGCGAATTCACCAACGTTTACATCAAAAACTTTGGGGATGACATGGATGATGAGAGACTGAAGGAGGTTTTCAGCAAGT
ATGGCCACCCCCTGAGTGTGAAGGTGATGAGAGACGCCAGCGGGAAATCCAAAGGCTTCGGCTTCGTGAGCTTCGAGAGC
CACCAGGCTGCCCAAAAGGCAGTTGAAGAAATGAACGGAAAGGACATAAACGGGCAGCCGGTTTTTGTGGGCAGGGCACA
AAAGAAAGGAGAGAGGCAGGCTGAGCTAAAGGAAATGTTTGAGCAGAAGAAAAAGGAAAGAATCCGTGGACGCCAGGGGG
TAAAACTGTACATTAAGAATCTGGACGATTCCATCGATGATGAGAAGCTACGGAAGGAGTTTTCTTCTTTTGGATCCATT
AACAGAGTGAAGGTAATGCAGGAGGAAGGGCAGAGCAAGGGGTTCGGCCTCATCTGCTTCTCCTCCTCCGAGGAGGCCCT
CGCAGCCATGGCTGAGATGAATGGCCGCATCTTGGGCTCCAAAGCCCTGAACATTGCCCTGGCCCAGAAGCAT

ORF - retro_itri_48 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.43 %
Parental protein coverage: 59.8 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI
Y.MASLYVGDLH.DVTE..L..KFS..GP.LSIR.CRD..TR.SLGYAYVNF.Q.ADA..ALDTMNFD.I
RetrocopyYRMASLYVGDLHVDVTEDLLFRKFSAVGPVLSIRICRDAVTRLSLGYAYVNFLQLADAQKALDTMNFDTI
ParentalKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFET
KGK..R.MWSQRD..LRKSGVGN.FIKNLDKSIDNK.L...FSAFG.ILS.KV..D..GSKGYGFVHF..
RetrocopyKGKSIRLMWSQRDAHLRKSGVGNVFIKNLDKSIDNKTLHEHFSAFGKILSSKVMSDDQGSKGYGFVHFQN
ParentalQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARA-KEFTNVYIKNFGEDMDDERLKDLFGKFGP
Q.AAE.AIE.MNG.LL.D..VFVGRFK.RKEREAEL...A..EFTNVYIKNFG.DMDDERLK..F.K.G.
RetrocopyQSAAEKAIEEMNGKLLKDCRVFVGRFKNRKEREAELRSKASSEFTNVYIKNFGDDMDDERLKEVFSKYGH
ParentalALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQD
.LSVKVM.D.SGKSKGFGFVSFE.H..AQKAV.EMNGK..NG....VGRAQKK.ERQ.ELK..FEQ.K..
RetrocopyPLSVKVMRDASGKSKGFGFVSFESHQAAQKAVEEMNGKDINGQPVFVGRAQKKGERQAELKEMFEQKKKE
ParentalRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGR
RI...QGV.LY.KNLDD.IDDE.LRKEFS.FG.I...KVM.E.G.SKGFG..CFSS.EEA..A..EMNGR
RetrocopyRIRGRQGVKLYIKNLDDSIDDEKLRKEFSSFGSINRVKVMQEEGQSKGFGLICFSSSEEALAAMAEMNGR
ParentalIVATKPLYVALAQR
I...K.L..ALAQ.
RetrocopyILGSKALNIALAQK

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






Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.
Ictidomys tridecemlineatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_itri_48 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_48 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus 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 10 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000158335 retrocopies
Homo sapiens ENSG000000707561 retrocopy
Macaca mulatta ENSMMUG000000177862 retrocopies
Monodelphis domestica ENSMODG000000062224 retrocopies
Mus musculus ENSMUSG000000222832 retrocopies
Oryctolagus cuniculus ENSOCUG000000043541 retrocopy
Pongo abelii ENSPPYG000000187903 retrocopies
Rattus norvegicus ENSRNOG000000086393 retrocopies
Sarcophilus harrisii ENSSHAG000000112671 retrocopy
Ictidomys tridecemlineatus ENSSTOG00000016395 2 retrocopies
retro_itri_139, retro_itri_48 ,



Copyright © RetrogeneDB 2014-2017