RetrogeneDB ID:

retro_ggor_1299

Retrocopy
location
Organism:Gorilla (Gorilla gorilla)
Coordinates:17:41361772..41362642(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPH1
Ensembl ID:ENSGGOG00000025844
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ggor_1299
ATGATGTTGGGCACCAAAGGTGGCGAGCGGTTTATGTTGAAGGTCCACGGCTTGCCCTGGTCTTGCTTGGCCGATGAAGT
GCAGCGTTTTTTTCTGACTGCAAAATTCAAAATAAGGCTCAAGGTATTCGTTTCATCTACAACAGAGAAGGCAGGCTGGG
TGACAAGGCTTTTGTTGAACTTGAATCAGAAGATGAAGTCAAATTGGCCCTGAAAAAGGACAGAGAAACTATGTGACACA
GTTTTGTTGAAGCATTCAAGTCAAACAACGTTGAAATGGATTGGGTGTTGAAGCATACCGGTCCAAATAGTCCTGACACG
GCCAGTGATGGCTTTGTACAGCTTAGAGGACTTCCCTTTGAATGCAGCAAAGAAGAAATTGTTCAGTTCTTCTCAGGGTT
GGAAATCGTACCAAATGGGATAACATTGCCAGTGGACTCCAGGGTGGGAGTACAGGGGAGGCCTTCGTGCAGTTTGCTTC
ACAGGAAATAACCAAAAAGGCTCTAAAGAAACACAAGGAAAGAATAGGGCACAGGTATATTGAAATCTTTAAGAGCAGCA
GGGCTGAAGTTAGAACTCACTACAATCCACCATAAAAGCTTATGGCCATGCAGCGGCCAGGTCCCATGACAGACCTGGTT
CTGGCAGAGGTTTTAACAGCATTGGCAGAGGAGCTGGCTTACAGAGGATGAGGCATGGTGCTTATGGTGGAGGATATGGA
GTCTATGACAATTATAATGGCTATGGCTATGGATTTGGGTCAGATAGATTTGGAAGAGACCTCAATTATTGTTTTTCAGG
AATGTCTGATCACAAATATGGGGATGGTGGCTCTACCTTCCAGAGCACAACAGGACACTGTATATACGTG

ORF - retro_ggor_1299 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.81 %
Parental protein coverage: 64.82 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMMLGTEGGEGFVVKVRGLPWSCSADEVQRFF-SDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKL
MMLGT.GGE.F..KV.GLPWSC.ADEVQRFF.SDCKIQN.AQGIRFIY.REGR....AFVELESEDEVKL
RetrocopyMMLGTKGGERFMLKVHGLPWSCLADEVQRFF<SDCKIQNKAQGIRFIYNREGRLGDKAFVELESEDEVKL
ParentalALKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPN
ALKKDRETM.H..VE.FKSNNVEMDWVLKHTGPNSPDTA.DGFV.LRGLPF.CSKEEIVQFFSGLEIVPN
RetrocopyALKKDRETM*HSFVEAFKSNNVEMDWVLKHTGPNSPDTASDGFVQLRGLPFECSKEEIVQFFSGLEIVPN
ParentalGITLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPG
GITLPVD..QG.STGEAFVQFASQEI..KALKKHKERIGHRYIEIFKSSRAEVRTHY.PP.KLMAMQRPG
RetrocopyGITLPVD<LQGGSTGEAFVQFASQEITKKALKKHKERIGHRYIEIFKSSRAEVRTHYNPP*KLMAMQRPG
ParentalP-YDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYG
P..DRPG.GRG.NSIGRGAG..RMR.GAYGGGYG.YD.YNGY..GYGFGSDRFGRDLNYCFSGMSDH.YG
RetrocopyP<HDRPGSGRGFNSIGRGAGLQRMRHGAYGGGYGVYDNYNGY--GYGFGSDRFGRDLNYCFSGMSDHKYG
ParentalDGGSTFQSTTGHCVHM
DGGSTFQSTTGHC...
RetrocopyDGGSTFQSTTGHCIYV

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .00 RPM 144 .05 RPM
SRP007412_cerebellum 0 .04 RPM 224 .10 RPM
SRP007412_heart 0 .00 RPM 78 .89 RPM
SRP007412_kidney 0 .00 RPM 227 .75 RPM
SRP007412_liver 0 .32 RPM 176 .73 RPM
SRP007412_testis 0 .73 RPM 349 .44 RPM

ChIP-Seq - click to see more details

Gorilla gorilla was not studied using ChIP-Seq data.

EST - click to see more details

Gorilla gorilla was not studied using EST data.

TSS - click to see more details

Gorilla gorilla was not studied using FANTOM5 data.

Lab - click to see more details

retro_ggor_1299 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ggor_1299 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000093891 retrocopy
retro_btau_130,
Canis familiaris ENSCAFG000000003362 retrocopies
retro_cfam_200, retro_cfam_230,
Choloepus hoffmanni ENSCHOG000000038414 retrocopies
retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Callithrix jacchus ENSCJAG000000099311 retrocopy
retro_cjac_127,
Dipodomys ordii ENSDORG000000054531 retrocopy
retro_dord_3,
Equus caballus ENSECAG000000144291 retrocopy
retro_ecab_94,
Echinops telfairi ENSETEG000000113031 retrocopy
retro_etel_50,
Gorilla gorilla ENSGGOG00000025844 2 retrocopies
retro_ggor_1299 , retro_ggor_177,
Myotis lucifugus ENSMLUG000000166251 retrocopy
retro_mluc_124,
Macaca mulatta ENSMMUG000000108431 retrocopy
retro_mmul_2,
Monodelphis domestica ENSMODG000000094363 retrocopies
retro_mdom_1301, retro_mdom_1302, retro_mdom_333,
Mustela putorius furoENSMPUG000000006931 retrocopy
retro_mputfur_156,
Mus musculus ENSMUSG000000078501 retrocopy
retro_mmus_142,
Nomascus leucogenys ENSNLEG000000266583 retrocopies
retro_nleu_1668, retro_nleu_28, retro_nleu_48,
Ochotona princeps ENSOPRG000000035131 retrocopy
retro_opri_11,
Procavia capensis ENSPCAG000000067151 retrocopy
retro_pcap_4,
Pteropus vampyrus ENSPVAG000000076701 retrocopy
retro_pvam_23,
Sorex araneus ENSSARG000000030241 retrocopy
retro_sara_29,
Sarcophilus harrisii ENSSHAG000000182041 retrocopy
retro_shar_674,
Ictidomys tridecemlineatus ENSSTOG000000163762 retrocopies
retro_itri_66, retro_itri_78,
Vicugna pacos ENSVPAG000000074852 retrocopies
retro_vpac_594, retro_vpac_614,


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