RetrogeneDB ID:

retro_pabe_110

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:100418743..100420093(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000020553
Aliases:HNRNPH2, HNRPH2
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPH1
Ensembl ID:ENSPPYG00000016121
Aliases:None
Description:heterogeneous nuclear ribonucleoprotein H1 (H) [Source:HGNC Symbol;Acc:5041]


Retrocopy-Parental alignment summary:






>retro_pabe_110
ATGATGCTGAGCACGGAAGGCAGGGAGGGGTTCGTGGTGAAGGTCAGGGGCCTACCCTGGTCCTGCTCAGCCGATGAAGT
GATGCGCTTCTTCTCTGATTGCAAGATCCAAAATGGCACATCAGGTATTCGTTTCATCTACACCAGAGAAGGCAGACCAA
GTGGTGAAGCATTTGTTGAACTTGAATCTGAAGAGGAAGTGAAATTGGCTTTGAAGAAGGACAGAGAAACCATGGGACAC
AGATACGTTGAAGTATTCAAGTCTAACAGTGTTGAAATGGATTGGGTGTTGAAGCATACAGGTCCGAATAGCCCTGATAC
TGCCAACGATGGCTTCGTCCGGCTTAGAGGACTCCCATTTGGCTGTAGCAAGGAAGAGATTGTTCAGTTCTTTTCAGGGT
TGGAAATTGTGCCAAATGGGATGACACTGCCAGTGGACTTTCAGGGGCGAAGCACAGGGGAAGCCTTTGTGCAGTTTGCT
TCACAGGAGATAGCTGAGAAGGCCTTAAAGAAACACAAGGAAAGAATAGGGCACAGGTACATTGAGATCTTCAAGAGTAG
CCGAGCTGAAGTTCGAACCCACTATGATCCCCCTCGAAAGCTCATGGCTATGCAGCGGCCGGGTCCCTATGATAGGCCGG
GGGCTGGCAGAGGGTATAATAGCATTGGCAGAGGAGCTGGGTTTGAAAGGATGAGGCGTGGTGCCTATGGTGGAGGGTAT
GGAGGCTATGATGACTATGGTGGCTATAATGATGGATATGGCTTTGGGTCTGATAGATTTGGAAGAGACCTCAATTACTG
TTTTTCAGGAATGTCTGATCATAGATACGGAGATGGTGGGTCCAGTTTCCAGAGCACCACAGGGCACTGTGTACACATGA
GGGGGTTACCTTACAGAGCCACTGAGAATGATATTTATAATTTCTTCTCACCTCTTAATCCCATGAGAGTACATATTGAA
ATTGGACCCGATGGCAGAGTTACCGGTGAGGCAGATGTTGAATTTGCTACTCATGAAGATGCTGTGGCAGCTATGGCAAA
AGACAAAGCTAATATGCAACACAGATATGTGGAGCTCTTCTTAAATTCTACTGCAGGAACAAGTGGGGGTGCTTACGATC
ACAGCTATGTAGAACTTTTTTTGAATTCTACAGCAGGGGCAAGTGGTGGCGCTTATGGTAGCCAAATGATGGGCGGGATG
GGCTTATCCAACCAGTCTAGTTATGGAGGTCCTGCTAGCCAGCAGCTGAGTGGTGGTTATGGAGGTGGTTATGGTGGTCA
GAGCAGTATGAGTGGATATGACCAAGTTCTGCAGGAAAACTCCAGTGACTATCAGTCAAACCTTGCTTAG

ORF - retro_pabe_110 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.89 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMMLGTDRSGEGFVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKL
MML.T....EGFVVKVRGLPWSCSADEV.RFFSDCKIQNG..GIRFIYTREGRPSGEAFVELESE.EVKL
RetrocopyMMLSTE-GREGFVVKVRGLPWSCSADEVMRFFSDCKIQNGTSGIRFIYTREGRPSGEAFVELESEEEVKL
ParentalALKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPN
ALKKDRETMGHRYVEVFKSN.VEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPN
RetrocopyALKKDRETMGHRYVEVFKSNSVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPN
ParentalGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGP
G.TLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGP
RetrocopyGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGP
ParentalYDRPGAGRG-NSIGRGAGFERXR-GAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDG
YDRPGAGRG.NSIGRGAGFER.R.GAYGGGYGGYDDY.GYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDG
RetrocopyYDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYGGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDG
ParentalGSTFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDK
GS.FQSTTGHCVHMRGLPYRATENDIYNFFSPLNP.RVHIEIGPDGRVTGEADVEFATHEDAVAAM.KDK
RetrocopyGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDK
ParentalANMQHRYVELFLNSTAGASGGAYEHRYVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSGG
ANMQHRYVELFLNSTAG.SGGAY.H.YVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSGG
RetrocopyANMQHRYVELFLNSTAGTSGGAYDHSYVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSGG
ParentalYGGGYGGQSSMSGYDQVLQENSSDFQSNIA
YGGGYGGQSSMSGYDQVLQENSSD.QSN.A
RetrocopyYGGGYGGQSSMSGYDQVLQENSSDYQSNLA

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 118 .43 RPM 105 .44 RPM
SRP007412_cerebellum 86 .46 RPM 191 .16 RPM
SRP007412_heart 53 .34 RPM 80 .17 RPM
SRP007412_kidney 78 .56 RPM 196 .56 RPM
SRP007412_liver 51 .59 RPM 135 .26 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_110 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_110 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_110 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 ENSPPYG00000016121 1 retrocopy
retro_pabe_110 ,
Pteropus vampyrus ENSPVAG000000076701 retrocopy
retro_pvam_23,
Rattus norvegicus ENSRNOG000000033991 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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