RetrogeneDB ID:

retro_itri_33

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393334.1:6085517..6087077(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000013325
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSTOG00000015009
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_itri_33
GTCAGCATGCTGCGCTTCCTGGTTCCCCGGCTGCTTTGCCTCCAGGGCAGGACTGCCCGGTACTTCTCAGCAGCAGCCCT
CCCAAGCCCAATCTCCAACCCAGACATCCGCTACAACCAGCTGTTCATCAACAACGAGTGGCAAGACGCAGTCAGCAAGA
AGACCTTCCCCACGGTCAACCCCACCACCGGTGAGGTCATCGGGCACGTGGCTGAAGGGGACAGGGCCGATGTGGACAGG
GCAGTGAAAGCAGCCCGTGAGGCCTTCCGCCTGGGGTCCCCGTGGCGCCGCATGGATGCATCTGAGCGGGGCCGGCTGTT
GAACCGCCTGGCAGACCTAGTGGAGCGGGATCGTGTCTACTTGGCCTCCCTGGAGACCTTGGACAACGGGAAGCCTTTCC
AAGAGTCTTACGCCTTGGACCTGGATGAGGTCATCAAGGTGTACCGCTACTTTGCCGGCTGGGCTGACAAGTGGCATGGC
AAGACCATCCCCATGGATGGCGAGCACTTCTGCTTCACCCGGCACGAGCCTGTGGGCGTCTGTGGCCAGATAATACCCTG
GAACTTCCCCTTGGTCATGCAAGGCTGGAAGCTGGCCCCGGCCCTGGCCACAGGCAACACCGTGGTCATGAAGGTTGCAG
AGCAGACCCCCCTTTCTGCCCTGTACCTGGCCTCCCTCATCAAGGAGGCCGGCTTTCCCCCTGGGGTGGTGAACATCATC
ACGGGCTACGGCCCAACAGCAGGAGCCGCCATCGCCCAGCACATGGATGTTGACAAAGTTGCCTTCACCGGCTCCACGGA
GGTGGGGCACCTGATCCAGAAGGCTGCCGGCGATTCCAACCTCAAGAGAGTCACCCTGGAGCTGGGTGGGAAGAGCCCCA
GCATCGTGTTGGCCGATGCCGACATGGGTCACGCCGTGGACCAGTGTCACGAAGCCCTCTTCTTCAACATGGGCCAGTGC
TGCTGCGCGGGGTCCCGGACCTTTGTCGAAGAATCCATCTACGATGAGTTTCTCGAGAGAACCGTGGAGAAGGCCAAGCA
GAGGAAAGTTGGGAACCCCTTTGAGCTGGACACCCAGCAGGGGCCCCAGGTGGACAAGGAGCAGTTTGAACGAATCCTGG
GCTACATCCGGCTGGGCCAGAAGGAGGGGGCAAAACTTCTTTGCGGTGGGGAGCGTTTTGGGGAGCGTGGTTTCTTCATC
AAGCCTACAGTCTTCGGTGGGGTGCAGGATGACATGACGATTGCCAAGGAGGAGATCTTTGGGCCCGTGCAGCCCCTGTT
CAAGTTCAAGAAGATCGAAGAGGTGATTGAGAGGGCCAACAACACCAGGTATGGCCTGGCTGCTGCCGTGTTCACCAGGG
ACCTGGACAAGGCCATGTACTTCACCCAGGCCCTGCAGGCCGGGACGGTGTGGGTGAACACCTACAACATCGTCACCTGC
CACACACCCTTCGGAGGCTTTAAGGAATCTGGCAATGGGAGGGAGCTGGGGGAGGATGGGCTTAGAGCCTACACGGAGGT
GAAGACTGTCACCATCAAGGTTCCTCAGAAAAACTCATGA

ORF - retro_itri_33 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.66 %
Parental protein coverage: 98.65 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLGPRLGC---RLLSAAATHAVPAPNQQPEVFYNQIFINNEWHDAVSKKTFPTVNPSTGEVICQVAEGNKE
L.PRL.C...R........A.P.P...P...YNQ.FINNEW.DAVSKKTFPTVNP.TGEVI..VAEG...
RetrocopyLVPRLLCLQGRTARYFSAAALPSPISNPDIRYNQLFINNEWQDAVSKKTFPTVNPTTGEVIGHVAEGDRA
ParentalDVDKAVKAARAAFQLGSPWRRMDASDRGRLLYRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLK
DVD.AVKAAR.AF.LGSPWRRMDAS.RGRLL.RLADL.ERDR.YLA.LETLDNGKP...SY..DLD.V.K
RetrocopyDVDRAVKAAREAFRLGSPWRRMDASERGRLLNRLADLVERDRVYLASLETLDNGKPFQESYALDLDEVIK
ParentalCLRYYAGWADKYHGKTIPMDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQT
..RY.AGWADK.HGKTIPMDG..F..TRHEPVGVCGQIIPWNFPL.MQ.WKL.PALATGN.VVMKVAEQT
RetrocopyVYRYFAGWADKWHGKTIPMDGEHFCFTRHEPVGVCGQIIPWNFPLVMQGWKLAPALATGNTVVMKVAEQT
ParentalPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEVGHLIQVAAGKSNLKRVTL
PL.ALY.A.LIKEAGFPPGVVNI..G.GPTAGAAIA.H.DVDKVAFTGSTEVGHLIQ.AAG.SNLKRVTL
RetrocopyPLSALYLASLIKEAGFPPGVVNIITGYGPTAGAAIAQHMDVDKVAFTGSTEVGHLIQKAAGDSNLKRVTL
ParentalELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYTEFLERSVARAKSRVVGNPFDS
ELGGKSP.I...DADM..AV.Q.H.ALFFN.GQCCCAGSRTFV.E.IY.EFLER.V..AK.R.VGNPF..
RetrocopyELGGKSPSIVLADADMGHAVDQCHEALFFNMGQCCCAGSRTFVEESIYDEFLERTVEKAKQRKVGNPFEL
ParentalRTEQGPQVDETQFKKILGYIQSGKQEGAKLLCGGEAAAERGYFIQPTVFGDVQDGMTIAKEEIFGPVMQI
.T.QGPQVD..QF..ILGYI..G..EGAKLLCGGE...ERG.FI.PTVFG.VQD.MTIAKEEIFGPV...
RetrocopyDTQQGPQVDKEQFERILGYIRLGQKEGAKLLCGGERFGERGFFIKPTVFGGVQDDMTIAKEEIFGPVQPL
ParentalLKFKTIEEVVGRANNSKYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGREL
.KFK.IEEV..RANN..YGLAAAVFT.DLDKA.Y..QALQAGTVWVN.Y.......PFGG.K.SG.GREL
RetrocopyFKFKKIEEVIERANNTRYGLAAAVFTRDLDKAMYFTQALQAGTVWVNTYNIVTCHTPFGGFKESGNGREL
ParentalGEYGLQAYTEVKTVTVKVPQKNS
GE.GL.AYTEVKTVT.KVPQKNS
RetrocopyGEDGLRAYTEVKTVTIKVPQKNS

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_33 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_33 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 21 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000136641 retrocopy
retro_amel_51,
Bos taurus ENSBTAG000000087431 retrocopy
retro_btau_48,
Canis familiaris ENSCAFG000000086831 retrocopy
retro_cfam_1493,
Equus caballus ENSECAG000000176732 retrocopies
retro_ecab_1054, retro_ecab_1061,
Felis catus ENSFCAG000000220001 retrocopy
retro_fcat_1590,
Homo sapiens ENSG000001112751 retrocopy
retro_hsap_19,
Gorilla gorilla ENSGGOG000000071081 retrocopy
retro_ggor_33,
Latimeria chalumnae ENSLACG000000117981 retrocopy
retro_lcha_108,
Microcebus murinus ENSMICG000000034871 retrocopy
retro_mmur_19,
Myotis lucifugus ENSMLUG000000170841 retrocopy
retro_mluc_1918,
Macaca mulatta ENSMMUG000000083361 retrocopy
retro_mmul_247,
Mustela putorius furoENSMPUG000000022821 retrocopy
retro_mputfur_27,
Mus musculus ENSMUSG000000294551 retrocopy
retro_mmus_222,
Nomascus leucogenys ENSNLEG000000000161 retrocopy
retro_nleu_22,
Otolemur garnettii ENSOGAG000000330931 retrocopy
retro_ogar_203,
Pongo abelii ENSPPYG000000049661 retrocopy
retro_pabe_32,
Pteropus vampyrus ENSPVAG000000131891 retrocopy
retro_pvam_163,
Rattus norvegicus ENSRNOG000000013441 retrocopy
retro_rnor_307,
Sus scrofa ENSSSCG000000098891 retrocopy
retro_sscr_9,
Ictidomys tridecemlineatus ENSSTOG00000015009 1 retrocopy
retro_itri_33 ,
Xenopus tropicalis ENSXETG000000209301 retrocopy
retro_xtro_12,


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