RetrogeneDB ID:

retro_rnor_340

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:X:105310739..105312089(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000011661
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Hnrph1
Ensembl ID:ENSRNOG00000003399
Aliases:Hnrnph1, Hnrph, Hnrph1
Description:heterogeneous nuclear ribonucleoprotein H [Source:RefSeq peptide;Acc:NP_543172]


Retrocopy-Parental alignment summary:






>retro_rnor_340
ATGATGCTGAGCACAGAGGGCAGGGAGGGGTTCGTGGTGAAGGTCAGGGGCCTACCCTGGTCCTGCTCAGCCGAGGAAGT
GATGCGCTTCTTTTCTGATTGCAAAATCCAAAATGGCACATCAGGTGTTCGTTTCATCTACACCAGAGAAGGCAGACCGA
GTGGTGAAGCATTTGTCGAACTCGAATCTGAAGATGAAGTGAAATTGGCTTTAAAGAAAGACAGAGAAACCATGGGACAC
AGATATGTTGAAGTATTCAAATCCAACAGTGTTGAAATGGATTGGGTGTTAAAGCATACAGGTCCAAATAGTCCTGATAC
TGCCAATGATGGGTTTGTACGGCTCAGAGGACTCCCATTTGGCTGTAGCAAGGAAGAAATTGTTCAGTTCTTTTCAGGGT
TGGAAATTGTGCCAAATGGGATGACACTGCCAGTGGACTTTCAGGGGCGGAGCACAGGGGAAGCTTTTGTGCAGTTTGCT
TCACAGGAGATAGCTGAAAAGGCCTTAAAGAAACACAAGGAAAGAATAGGGCATAGGTACATCGAGATCTTCAAGAGTAG
CAGAGCTGAAGTCCGAACCCACTATGATCCCCCTCGAAAGCTCATGACTATGCAGCGCCCGGGTCCTTATGATAGGCCAG
GGGCTGGGAGAGGGTATAATAGCATTGGCAGAGGAGCTGGGTTTGAAAGAATGAGGCGGGGTGCCTATGGTGGAGGGTAC
GGAGGCTATGATGACTACGGAGGTTATAATGACGGGTATGGTTTTGGGTCTGATAGATTTGGAAGAGACCTAAACTACTG
TTTCTCAGGAATGTCTGATCATCGATATGGAGATGGTGGGTCCAGTTTCCAGAGCACCACAGGGCACTGTGTACACATGA
GGGGGTTACCATACAGAGCCACTGAGAATGATATTTACAATTTTTTCTCACCTCTTAATCCCATGAGAGTACACATTGAA
ATCGGACCTGATGGCAGAGTCACGGGTGAGGCAGACGTTGAGTTTGCTACTCATGAAGACGCTGTGGCAGCTATGGCAAA
AGATAAAGCAAATATGCAGCACAGATATGTGGAGCTCTTCCTGAATTCTACCGCAGGGACGAGTGGAGGAGCTTATGATC
ATAGCTATGTAGAGCTCTTTTTGAATTCTACAGCAGGGGCAAGCGGTGGTGCTTATGGCAGCCAGATGATGGGAGGGATG
GGTTTATCCAACCAGTCTAGTTATGGAGGTCCAGCCAGCCAGCAGCTGAGTGCTGGCTACGGAGGTGGTTATGGTGGTCA
GAGCAGTATGAGCGGATATGACCAAGTTCTTCAGGAAAACTCAAGTGACTATCAGTCAAACCTTGCTTAG

ORF - retro_rnor_340 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.32 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMMLGAEGGEGFVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLA
MML..EG.EGFVVKVRGLPWSCSA.EV.RFFSDCKIQNG..G.RFIYTREGRPSGEAFVELESEDEVKLA
RetrocopyMMLSTEGREGFVVKVRGLPWSCSAEEVMRFFSDCKIQNGTSGVRFIYTREGRPSGEAFVELESEDEVKLA
ParentalLKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
LKKDRETMGHRYVEVFKSN.VEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
RetrocopyLKKDRETMGHRYVEVFKSNSVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
ParentalITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
.TLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLM.MQRPGPY
RetrocopyMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMTMQRPGPY
ParentalDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
DRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDY.GYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
RetrocopyDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYGGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
ParentalSTFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKA
S.FQSTTGHCVHMRGLPYRATENDIYNFFSPLNP.RVHIEIGPDGRVTGEADVEFATHEDAVAAM.KDKA
RetrocopySSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKA
ParentalNMQHRYVELFLNSTAGASGGAYEHRYVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSGGY
NMQHRYVELFLNSTAG.SGGAY.H.YVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLS.GY
RetrocopyNMQHRYVELFLNSTAGTSGGAYDHSYVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSAGY
ParentalGGGYGGQSSMSGYDQVLQENSSDFQSNIA
GGGYGGQSSMSGYDQVLQENSSD.QSN.A
RetrocopyGGGYGGQSSMSGYDQVLQENSSDYQSNLA

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
SRP017611_brain 66 .07 RPM 143 .29 RPM
SRP017611_kidney 58 .55 RPM 131 .33 RPM
SRP017611_liver 24 .14 RPM 73 .56 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

5 EST(s) were mapped to retro_rnor_340 retrocopy
EST ID Start End Identity Match Mis-match Score
CF111437 105310915 105311409 99.4 487 0 483
CR475043 105311470 105311780 100 310 0 310
DW309738 105311454 105311613 98.1 153 3 150
FM029514 105310976 105311278 100 302 0 302
FM061662 105310770 105311077 96.8 297 10 287

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_340 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_340 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 36 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000088882 retrocopies
retro_amel_57, retro_amel_9,
Bos taurus ENSBTAG000000093891 retrocopy
retro_btau_130,
Choloepus hoffmanni ENSCHOG000000038414 retrocopies
retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Callithrix jacchus ENSCJAG000000099311 retrocopy
retro_cjac_127,
Cavia porcellus ENSCPOG000000014855 retrocopies
retro_cpor_1065, retro_cpor_1094, retro_cpor_1095, retro_cpor_121, retro_cpor_711,
Equus caballus ENSECAG000000144291 retrocopy
retro_ecab_94,
Echinops telfairi ENSETEG000000113031 retrocopy
retro_etel_50,
Felis catus ENSFCAG000000012042 retrocopies
retro_fcat_131, retro_fcat_27,
Homo sapiens ENSG000001690452 retrocopies
retro_hsap_3322, retro_hsap_4911,
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,
Otolemur garnettii ENSOGAG000000126312 retrocopies
retro_ogar_208, retro_ogar_498,
Ochotona princeps ENSOPRG000000035131 retrocopy
retro_opri_11,
Procavia capensis ENSPCAG000000067151 retrocopy
retro_pcap_4,
Pongo abelii ENSPPYG000000161211 retrocopy
retro_pabe_110,
Pteropus vampyrus ENSPVAG000000076701 retrocopy
retro_pvam_23,
Rattus norvegicus ENSRNOG00000003399 1 retrocopy
retro_rnor_340 ,
Sorex araneus ENSSARG000000030241 retrocopy
retro_sara_29,
Sarcophilus harrisii ENSSHAG000000182041 retrocopy
retro_shar_674,
Sus scrofa ENSSSCG000000140221 retrocopy
retro_sscr_70,
Vicugna pacos ENSVPAG000000074852 retrocopies
retro_vpac_594, retro_vpac_614,


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