RetrogeneDB ID:

retro_pabe_42

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:3:36974510..36975902(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000013626
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPK
Ensembl ID:ENSPPYG00000019327
Aliases:HNRNPK, HNRPK
Description:Heterogeneous nuclear ribonucleoprotein K [Source:UniProtKB/Swiss-Prot;Acc:Q5R5H8]


Retrocopy-Parental alignment summary:






>retro_pabe_42
ATGGAAACTGAACATCCGGAAGAAAGCTTTCCTAACACTGAAACCAATGGTGAATTTGGTAAACGCCCTGCAGAAGATAT
GGAAGAGGAACAAGCATTTAAAAGGTCTAGAAACACTGATGAGATGGTTGAATTACGCATTCTGCTTCAGAGCAAGAATG
CCGGGGCAATGACTGGAAAAGGAGGCGAGAATATCAAGGCTCTCCCTACAGACTACAGTGCCAGTGTTTCAGTCCCAGAC
AGCAGTGGCCCCCAGCGCATATTGAGTATCAGTGCTGATATTGACACAATTGGAGAAATTCTGAAGAAAATCATCCCTAC
CTTGGAAGAGGGCCTGCAGTTGCCATCACCCACTGCAACCAGCCAGCTCCCTCTCGAACCTGATGCTGTGGAATGCTTAA
ATTACCAACACTATAAAGGAAGTGACTTTGACTACGAGTTGAGGCTGTTGATTCATCAGAGTCTAGCAGGAGGAATTATC
AGGGTCAAAGGTGTTAAAATCAAAGAACTTCGAGAGAACACTCAAACCACCATCAAGCTTTTCCAGGAATGCTGTCCTCA
TTCCACTGACAGAGTTGTTCTTATTGGAGGAAAACCCGATTGGGTTGTAGAGTGCATAAAGCTCATCCTTGATCTTATAT
CTGAGTCTCCCATCAAAGGACGTGCACAGCCTTATGATCGCAATTTTTACGATGAAACCTATGATTATGGTGGTTTTACA
ATGATGTTTGATGACCGCTTTGCACGCCCAGTGGGATTTCCCATGCGGGGGAGAGGTGGTTTTGACAGAACGCCTCCTGG
TCGGGGTGGGCGTCCCATGCTTACATCTAGAAGAGATTATGATGATATGAGCCCTCGTCCAGGACCACCTCCACCTCCTC
CCGGACGAGGCGGCCGGGGTGGTAGCAGAGCTCGGAATCTTCCTCTTCCTCCACCACCACCACCTAGAGGGGGAGACCTC
ATGGCCTATGACAGAAGAGGGAGACCTGGAGACCGTTACAACGGCGTGGTTGGTTTCAGTGCTGATGAAACTTGGGACTC
TGCAATAGACACATGGAGCCCATCAGAATGGCAGATGGTTTATGAGCCGCACGGTGGCCCCGGGTATGTTTATTCCTATG
CAGGGGGTCGTGGCTCATATGGTGATCTTGGTGGACCTATTATTACTACACAAGTAACGATTCCCAAAGATTTGGCTGGA
TCTATTATTGGCAAAGGTGGTCAGCGGATTAAACAAATCTGTCATGAGTCAGGAGCTTCGATCAAAATTGATGAGCCTTT
AGAAGGATCCGAAGATCGGATCATTACCATTACAGGAACACAGGAACAGATACAGAATGCACAGTATTTGCTGCAGAACA
GTGTGAAGCAGTATGCAGATGTTGAAGGATTC

ORF - retro_pabe_42 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.53 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMETEQPEETFPNTETNGEFGKRPAEDMEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRT
METE.PEE.FPNTETNGEFGKRPAEDMEEEQAFKRSRNTDEMVELRILLQSKNAGA..GKGG.NIKAL.T
RetrocopyMETEHPEESFPNTETNGEFGKRPAEDMEEEQAFKRSRNTDEMVELRILLQSKNAGAMTGKGGENIKALPT
ParentalDYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG
DY.ASVSVPDSSGP.RILSISADI.TIGEILKKIIPTLEEGLQLPSPTATSQLPLE.DAVECLNYQHYKG
RetrocopyDYSASVSVPDSSGPQRILSISADIDTIGEILKKIIPTLEEGLQLPSPTATSQLPLEPDAVECLNYQHYKG
ParentalSDFDCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKIIL
SDFD.ELRLLIHQSLAGGII.VKG.KIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPD.VVECIK.IL
RetrocopySDFDYELRLLIHQSLAGGIIRVKGVKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDWVVECIKLIL
ParentalDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRDY
DLISESPIKGRAQPYD.NFYDETYDYGGFTMMFDDR..RPVGFPMRGRGGFDR.PPGRGGRPM..SRRDY
RetrocopyDLISESPIKGRAQPYDRNFYDETYDYGGFTMMFDDRFARPVGFPMRGRGGFDRTPPGRGGRPMLTSRRDY
ParentalDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETWDSAID
DDMSPR.GPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRY.G.VGFSADETWDSAID
RetrocopyDDMSPRPGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYNGVVGFSADETWDSAID
ParentalTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGAS
TWSPSEWQM.YEP.GG.GY.YSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQI.HESGAS
RetrocopyTWSPSEWQMVYEPHGGPGYVYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQICHESGAS
ParentalIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYADVEGF
IKIDEPLEGSEDRIITITGTQ.QIQNAQYLLQNSVKQYADVEGF
RetrocopyIKIDEPLEGSEDRIITITGTQEQIQNAQYLLQNSVKQYADVEGF

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 1 .00 RPM 279 .55 RPM
SRP007412_cerebellum 0 .12 RPM 257 .55 RPM
SRP007412_heart 0 .09 RPM 133 .15 RPM
SRP007412_kidney 0 .33 RPM 269 .95 RPM
SRP007412_liver 0 .34 RPM 212 .77 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_42 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_42 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_42 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2674
Parental genes homology:
Parental genes homology involve 21 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000211312 retrocopies
retro_btau_468, retro_btau_605,
Dasypus novemcinctus ENSDNOG000000000264 retrocopies
retro_dnov_1433, retro_dnov_1820, retro_dnov_2316, retro_dnov_2638,
Dipodomys ordii ENSDORG000000160241 retrocopy
retro_dord_673,
Homo sapiens ENSG000001651193 retrocopies
retro_hsap_2323, retro_hsap_2674, retro_hsap_3385,
Loxodonta africana ENSLAFG000000265671 retrocopy
retro_lafr_809,
Macropus eugenii ENSMEUG000000069753 retrocopies
retro_meug_271, retro_meug_357, retro_meug_484,
Microcebus murinus ENSMICG000000157803 retrocopies
retro_mmur_1562, retro_mmur_235, retro_mmur_448,
Myotis lucifugus ENSMLUG000000058712 retrocopies
retro_mluc_128, retro_mluc_561,
Macaca mulatta ENSMMUG000000188711 retrocopy
retro_mmul_2111,
Monodelphis domestica ENSMODG000000084021 retrocopy
retro_mdom_1666,
Mus musculus ENSMUSG000000215462 retrocopies
retro_mmus_1131, retro_mmus_2137,
Nomascus leucogenys ENSNLEG000000034863 retrocopies
retro_nleu_1178, retro_nleu_1815, retro_nleu_973,
Otolemur garnettii ENSOGAG000000074783 retrocopies
retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii ENSPPYG000000045812 retrocopies
retro_pabe_3346, retro_pabe_92,
Pongo abelii ENSPPYG00000019327 3 retrocopies
retro_pabe_2105, retro_pabe_2106, retro_pabe_42 ,
Sarcophilus harrisii ENSSHAG000000171091 retrocopy
retro_shar_820,
Sus scrofa ENSSSCG000000227601 retrocopy
retro_sscr_437,
Tupaia belangeri ENSTBEG000000012891 retrocopy
retro_tbel_2491,
Tarsius syrichta ENSTSYG000000011963 retrocopies
retro_tsyr_1664, retro_tsyr_1796, retro_tsyr_2149,
Tursiops truncatus ENSTTRG000000049061 retrocopy
retro_ttru_1622,
Tursiops truncatus ENSTTRG000000166937 retrocopies
retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,


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