RetrogeneDB ID:

retro_itri_460

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393293.1:14544764..14545864(+)
Located in intron of:ENSSTOG00000021107
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DRG1
Ensembl ID:ENSSTOG00000014187
Aliases:None
Description:developmentally regulated GTP binding protein 1 [Source:HGNC Symbol;Acc:3029]


Retrocopy-Parental alignment summary:






>retro_itri_460
ATGAGTAGCACTTTAGCAAAGATCGCAGAGATCAAAGCCGAGATGGCTCGGACTCAAAAGAACAAGGCAACAGCACACCA
CCTAGGGCTGCTTAAGGCTCGCCTTGCTAAGCTTCGTAGAGAACTCATTACTCCAAAAGGTGGTAGAGGTGGTGGGCCAG
GAGAAGGTTTTGATGTGGCCAACACTGGTGATCTCGAATTAAGTCTGTGGGTTTTCCATCTGTGGGGAAGTCAACACTAC
TGAGTAACTTGGCTGGGGTATATTCTGAAATGGCAGCCTATGAATTTACTACCCTAACTACTGTGCCTGGTGTCATCACA
TACAAAGGTGCCAAAAAACAGCTTCTGGAACTCCCAGGTATCATTGAAGGTGCCAAGGATGGGAAAGGTAGGGGCTGTCA
GGTTATTGCAGTGACCTGAGCATGCAATTTGATCCTGATTGTTCTGGAAGTCCTGAAGCCACTAGGACATAAGAAGGTAA
CTGAAAATGAATTGGAAGGCTTTGGTATTTGCTTGAATAGTAAACCTCCCAACATTGGCTTTAAGAAGAAAGATAAAGGA
GGCATTAATCTCACAACTACCTGCCCTCAGAGTGAGCTGGATGCTGAAACTGTGAAGAGCATTCTTGCTAAATACAAAAT
TCATAATGCTGATGTGACTTTGCGTAGTAATGCCACAGCTGATGACTTCATTGATGTGGTGGAAGGAAACAGGGTTTATA
TTCCTTGTATTTATGTATTAAATAAAATCGATCAAATCTCCATTGAGGAATTGGATATCATCTATAAAGTGCCTCACTGT
GTACCCATCTCTGCCCATCACCGCTGGAATTTTGATGACCTGTTAGAAAAGATCTGGGACTATTTGAAACTAGTGAGAAT
TTACACCAAACCCAAAGGCCAGTTACCAGATTACACATCTCCAGTGGTGCTGCCTTACTCCAGGACCACGGTGAAGGATT
TCTGCATGAAGATCCACAAAAATCTTATCAAAGAATTTAAATACGCTCTGGTCTGGGGTCTCTCTGTGAAACACAATCCA
CAGAAAGTGGGTAACGACCATACATTGGAGGACGAGGATGTCATTCAGATTGTGAAGAAA

ORF - retro_itri_460 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.22 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMSSTLAKIAEIEAEMARTQKNKATAHHLGLLKARLAKLRRELITPKGGGGGGPGEGFDVAKTGD-ARIGF
MSSTLAKIAEI.AEMARTQKNKATAHHLGLLKARLAKL............GGPGEGFDVA.TGD..RI..
RetrocopyMSSTLAKIAEIKAEMARTQKNKATAHHLGLLKARLAKLXXXXXXXXXXXXGGPGEGFDVANTGD<SRIKS
ParentalVGFPSVGKSTLLSNLAGVYSEVAAYEFTTLTTVPGVIRYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVA
VGFPSVGKSTLLSNLAGVYSE.AAYEFTTLTTVPGVI.YKGAK.QLL.LPGIIEGAKDGKGRG.QVIAV.
RetrocopyVGFPSVGKSTLLSNLAGVYSEMAAYEFTTLTTVPGVITYKGAKKQLLELPGIIEGAKDGKGRGCQVIAVT
ParentalRTCNLILIVLDVLKPLGHKKIIENELEGFGIRLNSKPPNIGFKKKDKGGINLTATCPQSELDAETVKSIL
..CNLILIVL.VLKPLGHKK..ENELEGFGI.LNSKPPNIGFKKKDKGGINLT.TCPQSELDAETVKSIL
Retrocopy*ACNLILIVLEVLKPLGHKKVTENELEGFGICLNSKPPNIGFKKKDKGGINLTTTCPQSELDAETVKSIL
ParentalAEYKIHNADVTLRSDATADDLIDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCVPISAHHRWNFD
A.YKIHNADVTLRS.ATADD.IDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCVPISAHHRWNFD
RetrocopyAKYKIHNADVTLRSNATADDFIDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCVPISAHHRWNFD
ParentalDLLEKIWDYLKLVRIYTKPKGQLPDYTSPVVLPYSRTTVEDFCMKIHKNLIKEFKYALVWGLSVKHNPQK
DLLEKIWDYLKLVRIYTKPKGQLPDYTSPVVLPYSRTTV.DFCMKIHKNLIKEFKYALVWGLSVKHNPQK
RetrocopyDLLEKIWDYLKLVRIYTKPKGQLPDYTSPVVLPYSRTTVKDFCMKIHKNLIKEFKYALVWGLSVKHNPQK
ParentalVGKDHTLEDEDVIQIVKK
VG.DHTLEDEDVIQIVKK
RetrocopyVGNDHTLEDEDVIQIVKK

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_460 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_460 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 17 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000070401 retrocopy
retro_amel_1448,
Canis familiaris ENSCAFG000000326016 retrocopies
retro_cfam_1535, retro_cfam_1807, retro_cfam_382, retro_cfam_415, retro_cfam_453, retro_cfam_607,
Ciona intestinalis ENSCING000000033051 retrocopy
retro_cint_1,
Callithrix jacchus ENSCJAG000000110094 retrocopies
retro_cjac_1104, retro_cjac_2246, retro_cjac_2606, retro_cjac_855,
Cavia porcellus ENSCPOG000000107911 retrocopy
retro_cpor_1401,
Ciona savignyi ENSCSAVG000000065031 retrocopy
retro_csav_10,
Dasypus novemcinctus ENSDNOG000000013121 retrocopy
retro_dnov_531,
Homo sapiens ENSG000001857211 retrocopy
retro_hsap_2231,
Gorilla gorilla ENSGGOG000000111851 retrocopy
retro_ggor_1665,
Myotis lucifugus ENSMLUG000000070331 retrocopy
retro_mluc_1447,
Macaca mulatta ENSMMUG000000190991 retrocopy
retro_mmul_999,
Mustela putorius furoENSMPUG000000128101 retrocopy
retro_mputfur_339,
Mus musculus ENSMUSG000000204571 retrocopy
retro_mmus_2366,
Nomascus leucogenys ENSNLEG000000270011 retrocopy
retro_nleu_2627,
Pan troglodytes ENSPTRG000000142721 retrocopy
retro_ptro_1578,
Ictidomys tridecemlineatus ENSSTOG00000014187 1 retrocopy
retro_itri_460 ,
Tarsius syrichta ENSTSYG000000101603 retrocopies
retro_tsyr_1374, retro_tsyr_1918, retro_tsyr_405,


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