RetrogeneDB ID:

retro_itri_170

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393557.1:1129828..1131214(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000022742
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:LSM14A
Ensembl ID:ENSSTOG00000002785
Aliases:None
Description:LSM14A, SCD6 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:24489]


Retrocopy-Parental alignment summary:






>retro_itri_170
ATGAGCTGGGGCACCCCTTACCTCGGCAGCAACATTAGCCTCATCTCTAAAGCGGAGATCCGCTATGAGGGCATCCTCTA
CACCATCGACACCGAGAACTCCACTATAGCCCTCGCCAAAGTTCGATCCTTTGGTACAGAAGACAGACCAACAGATCGGC
CCGTACCACCTCGAGATGAAGTCTTTGAATATATTATCTTCCGTGGGAATGATATTAAAGATCTGACCGTTTGCGAGCCT
CCCAAACCACAATGTTCTTTGCCTCAGGACTCAGCTATCATTCAGTCTTCGCTAGGTTCGTCTCCGTTCCAGTCAGTGGG
TTCCTACGGACCTTTTGGCAGCATGCCCATGTACAGTCAGTTCAGTCTAAGTTCATTGGTCGGGCAGCAGTTTGGTGCTC
TTGGTGTTGCTGGAAGCTCCTTGCCATCCTTTGGAATGGAGACATCAAACAGTGATACCTTATCCCAAAGTAGTGCAATT
GGTTCTGCCTTTATACAGGATACAAGAACTATAAAAACACAGTCATTTCAAGGTCGTTCAAGCCCTCAGTTAGACCCTTT
GAGAGAAAGTCCAACCATGGAACAAGCAGTACAGACTGCCCCGGCCCACTTACCTGCTCCAGCACCTGTTGGGAGAAGGA
GCCCTGTATCAACCCCGCCTTTGCCATCTACCGGCCAAAAAACAATAGAGAATCAAGAGCACAAGCAAGCTGAAGTACCC
AACGTTTCAAGGTCAGAAAATGAGCAACTCAGAAATCATAGTAAGAGACAAGTAGTTCCAGGTGCTTCGTCAGCTCCAAG
AAAAGGGCGTGGGGGTCATCGATGTGGCAGGAGATTTGGTATTCAGCGATATGGTCCAATGAAATTTGAGAATGACTTTG
ACTTTGAACGTGCAAATGCACAATTTAACAAGGAGGAGATTGACAGAGAGTTTCATAATAAACTGAAATTAAAAGAAGAT
AAACTTCAGAAAAAAGAGAAGCCAGTAAATGGTGAAGGTAAAGGAGTTGATACCCAAAACAGTGAAGAAGACACTGATGA
AGAAGATCCACTTGGACCTAATTGCTATTATGACAAAAGTAAATCCTTCTTTGACAATATTTCTTATAATATTAATAGGG
AACAGAGGCCAACCTGGGCTGAAGAAAGAAGATTAAATGCTGAAACATTTGGAATTCCACTTCATCCAAACCATGGTGGT
GGGAGGTACAGAAGCAGAAGAGGTCTGAGTTTCCGTGGCAACAGAAGGCCTAGTGGTGGCAGAGGTGGCACATTTACTAC
CCCTCGAGGATTTCACTGGGGTTTTCACCGCGGATTCCGAAGAGGGCACTGGGGCAGGGAGTTTGCAGATTTTGAATACA
GGAAAAACAACAAAGTTGCTGCATAG

ORF - retro_itri_170 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.45 %
Parental protein coverage: 98.27 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMPTYSQFSPSSLVGQQFGAVGVAGSSLTSFGTETSNSGTLSQSSAVGSAFTQDTRSIKTQLSQGRSSPQL
MP.YSQFS.SSLVGQQFGA.GVAGSSL.SFG.ETSNS.TLSQSSA.GSAF.QDTR.IKTQ..QGRSSPQL
RetrocopyMPMYSQFSLSSLVGQQFGALGVAGSSLPSFGMETSNSDTLSQSSAIGSAFIQDTRTIKTQSFQGRSSPQL
ParentalDPLRKSPTMEQAVQTASAHLPAPAPVGRRSPVSTRPLPSTSQKAIENQEHRRAEVHKVSRPENEQLRNDN
DPLR.SPTMEQAVQTA.AHLPAPAPVGRRSPVST.PLPST.QK.IENQEH..AEV..VSR.ENEQLRN..
RetrocopyDPLRESPTMEQAVQTAPAHLPAPAPVGRRSPVSTPPLPSTGQKTIENQEHKQAEVPNVSRSENEQLRNHS
ParentalKRQVVPGASSAPRRGRGGHRGGRGRFGIRRDGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLE
KRQVVPGASSAPR.GRGGHR.GR.RFGI.R.GPMKFE.DFDFE.ANAQFNKEEIDREFHNKLKLKEDKL.
RetrocopyKRQVVPGASSAPRKGRGGHRCGR-RFGIQRYGPMKFENDFDFERANAQFNKEEIDREFHNKLKLKEDKLQ
ParentalKQEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYDKTKSFFDNISCDDNRERRPTWAEERRLNAETF
K.EKPVNGE.KG...VDTQNSE...DEEDPLGPNCYYDK.KSFFDNIS...NRE.RPTWAEERRLNAETF
RetrocopyKKEKPVNGEGKG---VDTQNSEEDTDEEDPLGPNCYYDKSKSFFDNISYNINREQRPTWAEERRLNAETF
ParentalGIPLRPNRGRGGYRGRGGLGFRGGRGRGGGRGGTFTTPRGFRGGF----RGGRGGREFADFEYRK
GIPL.PN.G.G.YR.R.GL.FRG.R...GGRGGTFTTPRGF..GF....R.G..GREFADFEYRK
RetrocopyGIPLHPNHGGGRYRSRRGLSFRGNRRPSGGRGGTFTTPRGFHWGFHRGFRRGHWGREFADFEYRK

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






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_170 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_170 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 13 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000065551 retrocopy
retro_chof_1375,
Callithrix jacchus ENSCJAG000000103605 retrocopies
retro_cjac_1582, retro_cjac_2625, retro_cjac_3201, retro_cjac_3327, retro_cjac_840,
Gorilla gorilla ENSGGOG000000017621 retrocopy
retro_ggor_2378,
Microcebus murinus ENSMICG000000115981 retrocopy
retro_mmur_1605,
Myotis lucifugus ENSMLUG000000033681 retrocopy
retro_mluc_1793,
Macaca mulatta ENSMMUG000000216142 retrocopies
retro_mmul_1386, retro_mmul_1860,
Nomascus leucogenys ENSNLEG000000117134 retrocopies
retro_nleu_1299, retro_nleu_2544, retro_nleu_2580, retro_nleu_485,
Oryctolagus cuniculus ENSOCUG000000118722 retrocopies
retro_ocun_193, retro_ocun_860,
Otolemur garnettii ENSOGAG000000024922 retrocopies
retro_ogar_2586, retro_ogar_67,
Pongo abelii ENSPPYG000000098322 retrocopies
retro_pabe_1693, retro_pabe_2906,
Pan troglodytes ENSPTRG000000108133 retrocopies
retro_ptro_1343, retro_ptro_2389, retro_ptro_863,
Rattus norvegicus ENSRNOG000000211331 retrocopy
retro_rnor_2397,
Ictidomys tridecemlineatus ENSSTOG00000002785 1 retrocopy
retro_itri_170 ,


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