RetrogeneDB ID:

retro_pabe_2750

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:75981253..75982352(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KPNA7
Ensembl ID:ENSPPYG00000017369
Aliases:None
Description:karyopherin alpha 7 (importin alpha 8) [Source:HGNC Symbol;Acc:21839]


Retrocopy-Parental alignment summary:






>retro_pabe_2750
CTGAAGTCATCACTTTACCTCTGCTTGCAGTTGAGGCCACTGGGCCTGACCAACATTGCTTCAGGGACTCCGAGCAGATT
TGAGCCGTGGTAGAAGGGGGACCCATCCAGCCCTTGATCAAGCTCCTGTCTTCCCCCAATGTGGCTGTGTGTGAACAGGC
AATGTGGGCTCTTGGTAATATACCTGGTGATGGCCTGGAGTTTAGAGATAATGTCATCTCAAGCAATGCCATCCCACATC
TGCTGGCCTTGATTTCACCCACCCTACCAATCACATTTCTGCGGAACATCACGTGGACCTTGTCGAACCTATGCCGAAAA
AAGACCCCGTACTCTTGCGAAACTGCAGTGAAGCAGATGCTGCGTGCCCTCTTACTCCTGCAGCGCCACGACAGCGAGGT
TGTCTCGGAAGCCTGCTGGTCACTGTCCTACCTCACCGACGGCTGCAAAGAGCTCATCAGCCAAGTGGATGACACAGGGG
TCCTGCTCAGGCTGGTAGCCCTCATGACCATCTCAGAACTCAATGTCTGGACCCCTTCTCTCCCGTACCATGGGGAACAC
TATCACAGGCACAGATGAACAGAAGCAGATGGCCATTGACGCAGGCATGCTGAACGTGCTGCCCCAGTTCCTGCAGCACA
ACAAGCCCTCCATCCAGGAGGCGGCCTGGGCCCTGAGCAACGTGGCGGCAGGGCCCTCTCACCACACCCAGCAGCTGCTT
GTCTACAACCTCTTGCCTCCCGTGGTGGCTCTGCTAAAAAAAAAATGGAGAATTTAAAGTCCAGAAAGAGGCTGTCTGGA
CGGTGGCTAACTTTGCAATGTGGGTCACCGTGGATAAGCTGATCCCCTATTCTGGGGTCCTGGAGCCACTGGTGAATCTG
CTCATTGCCCCAGATGTTAAAATTGTTCTCATCATCCTCGATGTAATCTCTTGCATCCTCCAGTCGTCAGAGAAACGGTC
TGAGAAGGAAATCCTATGTTTTCTGATAGAAGAACTTGGTAGGATCGATAGAATTGAGGCTTTACAACTGCATGAGAACT
GTCAGATTGGCCAGTCTGCTTTGAACATCATTGAGAAGCACTTTGGTGAGGAAGAAGAT

ORF - retro_pabe_2750 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.8 %
Parental protein coverage: 73.56 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLKSSLYPCLQFEAAWALTNIASGT-SEQTRAVVEGGAIQPLIELLSSSNVAVCEQAVWALGNIAGDGPEF
LKSSLY.CLQ......LTNIASGT.SEQ..AVVEGG.IQPLI.LLSS.NVAVCEQA.WALGNI.GDG.EF
RetrocopyLKSSLYLCLQLRPL-GLTNIASGT<SEQI*AVVEGGPIQPLIKLLSSPNVAVCEQAMWALGNIPGDGLEF
ParentalRDNVITSNAIPHLLALISPTLPITFLRNITWTLSNLCRNKNPYPCDTAVKQILPALLHLLQHQDSEVLSD
RDNVI.SNAIPHLLALISPTLPITFLRNITWTLSNLCR.K.PY.C.TAVKQ.L.ALL.LLQ..DSEV.S.
RetrocopyRDNVISSNAIPHLLALISPTLPITFLRNITWTLSNLCRKKTPYSCETAVKQMLRALL-LLQRHDSEVVSE
ParentalACWALSYLTDGSNKRIGQVVDTGVLPRLVVLMTSSELNVLTPSL-RTVGNIVTGTDEQTQMAIDAGMLNV
ACW.LSYLTDG....I.QV.DTGVL.RLV.LMT.SELNV.TPSL.RT.GN..TGTDEQ.QMAIDAGMLNV
RetrocopyACWSLSYLTDGCKELISQVDDTGVLLRLVALMTISELNVWTPSL>RTMGNTITGTDEQKQMAIDAGMLNV
ParentalLPQLLQHNKPSIQKEAAWALSNVAAGPCHHIQQLL-AYDVLPPLVALLKNGEFKVQKEAVWTVANFATGA
LPQ.LQHNKPSIQ..A.......A....H..Q.L......LP........GEFKVQKEAVWTVANFA...
RetrocopyLPQFLQHNKPSIQEAAWALSNVAAGPSHHTQQLLV>TTSCLPWWLCXXXXGEFKVQKEAVWTVANFAMWV
ParentalTMDQLIQLVHSGVLEPLVNLLTAPDVKIVLIILDVISCILQAAEKRSEKENLCLLIEELGGIDRIEALQL
T.D.LI....SGVLEPLVNLL.APDVKIVLIILDVISCILQ..EKRSEKE.LC.LIEELG.IDRIEALQL
RetrocopyTVDKLIP--YSGVLEPLVNLLIAPDVKIVLIILDVISCILQSSEKRSEKEILCFLIEELGRIDRIEALQL
ParentalHENRQIGRSALNIIEKHFGEVSD
HEN.QIG.SALNIIEKHFGE..D
RetrocopyHENCQIGQSALNIIEKHFGEEED

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 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .83 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_2750 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2750 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2750 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3337
Pan troglodytes retro_ptro_2142
Parental genes homology:
Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000151252 retrocopies
retro_cfam_459, retro_cfam_861,
Choloepus hoffmanni ENSCHOG000000042431 retrocopy
retro_chof_805,
Callithrix jacchus ENSCJAG000000159431 retrocopy
retro_cjac_2964,
Equus caballus ENSECAG000000005541 retrocopy
retro_ecab_981,
Echinops telfairi ENSETEG000000000961 retrocopy
retro_etel_1548,
Homo sapiens ENSG000001854671 retrocopy
retro_hsap_3337,
Mus musculus ENSMUSG000000387702 retrocopies
retro_mmus_2844, retro_mmus_3301,
Nomascus leucogenys ENSNLEG000000108271 retrocopy
retro_nleu_1680,
Otolemur garnettii ENSOGAG000000311063 retrocopies
retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Ochotona princeps ENSOPRG000000154342 retrocopies
retro_opri_1101, retro_opri_118,
Pongo abelii ENSPPYG000000085691 retrocopy
retro_pabe_3501,
Pongo abelii ENSPPYG00000017369 1 retrocopy
retro_pabe_2750 ,
Pan troglodytes ENSPTRG000000194462 retrocopies
retro_ptro_102, retro_ptro_2142,
Tupaia belangeri ENSTBEG000000090073 retrocopies
retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,
Tursiops truncatus ENSTTRG000000029982 retrocopies
retro_ttru_1426, retro_ttru_430,


Copyright © RetrogeneDB 2014-2017