RetrogeneDB ID:

retro_itri_350

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393285.1:16812453..16812775(-)
Located in intron of:ENSSTOG00000027189
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CNEP1R1
Ensembl ID:ENSSTOG00000001179
Aliases:None
Description:CTD nuclear envelope phosphatase 1 regulatory subunit 1 [Source:HGNC Symbol;Acc:26759]


Retrocopy-Parental alignment summary:






>retro_itri_350
CGAAGACTTTGTGAATCCATTCAGCCTTTGTCTCCTGCTCCAGGATCCTGGAGAATGCTTCTCATGGAGGCATGTCTCTG
CCTAGGTGCCTGGAACGAGTTAATAGATCCCGAGACACCAAAAGGTCCTTCTTTGCATCTTTATGGAGTCGTGCCATTTT
TTACCATTAGCTTTTCACTCTAATAGGTTTATTCTTTGCTGGGTACACAAGAGAGTAGTTGTGCCATCAATTATAGCAGC
TCAATGTCAAACAGCATTAGCAGAGTATAAACACGTCCGTGATGATACAGGGAAACCAATTTTGAAATCTAGGCCTTCTG
TT

ORF - retro_itri_350 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.79 %
Parental protein coverage: 88.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalRRLTEYIHCLQPATGRWRMLLIVVSVCTATGAWNWLIDPETQKV-SFFTSLWNH-PFFTIS-CITLIGLF
RRL.E.I..L.PA.G.WRMLL.....C...GAWN.LIDPET.K..SFF.SLW...PFFTIS...TLIGLF
RetrocopyRRLCESIQPLSPAPGSWRMLLM--EACLCLGAWNELIDPETPKG<SFFASLWSR>PFFTIS<LFTLIGLF
ParentalFAG-IHKRVVAPSIIAARCRTVLAEYNMSCDDTGKLILKPRPHV
FAG..HKRVV.PSIIAA.C.T.LAEY....DDTGK.ILK.RP.V
RetrocopyFAG<VHKRVVVPSIIAAQCQTALAEYKHVRDDTGKPILKSRPSV

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_350 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_350 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 23 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000064911 retrocopy
retro_amel_732,
Callithrix jacchus ENSCJAG000000019971 retrocopy
retro_cjac_4204,
Cavia porcellus ENSCPOG000000127911 retrocopy
retro_cpor_669,
Erinaceus europaeus ENSEEUG000000057371 retrocopy
retro_eeur_211,
Felis catus ENSFCAG000000239361 retrocopy
retro_fcat_1713,
Homo sapiens ENSG000002054231 retrocopy
retro_hsap_4886,
Gorilla gorilla ENSGGOG000000252111 retrocopy
retro_ggor_3051,
Loxodonta africana ENSLAFG000000125731 retrocopy
retro_lafr_907,
Myotis lucifugus ENSMLUG000000069002 retrocopies
retro_mluc_1437, retro_mluc_2115,
Macaca mulatta ENSMMUG000000083653 retrocopies
retro_mmul_1586, retro_mmul_1873, retro_mmul_2624,
Mustela putorius furoENSMPUG000000031091 retrocopy
retro_mputfur_453,
Nomascus leucogenys ENSNLEG000000007272 retrocopies
retro_nleu_1341, retro_nleu_831,
Oryctolagus cuniculus ENSOCUG000000059231 retrocopy
retro_ocun_1267,
Otolemur garnettii ENSOGAG000000156651 retrocopy
retro_ogar_2835,
Pongo abelii ENSPPYG000000073353 retrocopies
retro_pabe_1396, retro_pabe_2430, retro_pabe_3799,
Pan troglodytes ENSPTRG000000416821 retrocopy
retro_ptro_3255,
Ictidomys tridecemlineatus ENSSTOG00000001179 1 retrocopy
retro_itri_350 ,


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