RetrogeneDB ID:

retro_pabe_2111

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:2b:43253092..43254287(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DNAJA1
Ensembl ID:ENSPPYG00000019141
Aliases:None
Description:DnaJ homolog subfamily A member 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5NVI9]


Retrocopy-Parental alignment summary:






>retro_pabe_2111
ATGGTGAAATAAACCACTTTCCATGATTTTTAGAGGGTCAAACAAAGTACCACTAAGGAAGAATTTAAAAAGGCTTATAG
GAAACTGGCCTTGAAGTACCACCCTGATAAAAATCCAAATGGAGAGAAGTTTAAACGAATTTCTCAAACTTACAAAGTTA
TTTCTGATGCCAAGAAAAGGGAATTATACAACAAAGGAAGATAACAGGTAAATAAGAGCGCTGAGCAAGTGGCAGTTCTG
GGTCCCCTATGGACATCTTCAACATAATTATTTATGGAGGAAGAAGAATGCAGAGAGAAAAGAGGAGTAACATTGTTGTG
CATCAGCTCTCAAAAACCTTAGAAAATGTATGTGATGGTACAACAAGAAAATTGGCACTTCACAAGAATGTAATTTGTGA
CTAATGTGAAGGCAGAAGTGGGGAAAAAAAGAGGAGAGAAGGATAGTGTTGTCCCAATTGCCAAGTTACTGGACTGCAAA
TAAGAATTCATGCAATAGGGCCTGGGATGGTTCAGCACACTTAGTCTGTGTGCATGCATGGAGTGCCACGGTCATGGAGA
ATGAATCAGTCCTAAAGATAGATGTAAACACGAAAATGGAAGAAAGATAGTTTGAGGGAAAAAGATTCTAGAAGTTCATG
TTGACAATGACATGAAATATGGCCAGAAGATAACATTTCATGGTGAAGGAGACAAAGAACCCGGATTGGAGCCAGGAGAT
ATTATCATTGAGTTAGATGAAAAGGACCATGCTGTTTTTACTTGACAAGAAGACTAGTTTATGTCTATGGACAGACAGCT
GGTTAAAATATTGTGTGGTTTCCAAAAACCAATATCCACTCTTGATTACTGAACTATAGTCATCACCTCTCACCCAGGTC
AGACTGTCAAATATGGAGAAATCAAATGTGTGCTAAATGAAGTCATGCCAATTTTTCATAGACCATATGAAAAGCATCAC
CTAATCATCAAATTCAAGGTAAACTTTCCTGAGAATGGTTTTCTCTCTCATGATAAGCTCTCTTAGTTGGGTAAACTCCT
ACCTGACAGGAAGGAAATAGAAGAGATTGTTGAAATGGATCAAGTTAAAACTGGTGTACTTTGATTCAGATCAGGAAAAA
CAGCACTATTGCAATGGAGAAACATGTGAGGATGATAAACATCATCCCAGAGGCGGTGTTCACTGCCAAACTTCA

ORF - retro_pabe_2111 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.22 %
Parental protein coverage: 100. %
Number of stop codons detected: 13
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKGGEQ
MVK.TT..D...VK...T.EE.KKAYRKLALKYHPDKNPN.GEKFK.ISQ.Y.V.SDAKKRELY.KG..Q
RetrocopyMVK*TTFHDF*RVKQSTTKEEFKKAYRKLALKYHPDKNPN-GEKFKRISQTYKVISDAKKRELYNKGR*Q
ParentalAIK-EGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEG
..K.E..A.G..GSPMDIF.....GG.RMQRE.R...VVHQLS.TLE....G.TRKLAL.KNVICD.CEG
RetrocopyVNK<ER*ASGSSGSPMDIFNIIIYGGRRMQREKRSNIVVHQLSKTLENVCDGTTRKLALHKNVICD*CEG
ParentalRGGKKGAVE--CCPNCRGTGMQIRIH-QIGPGMVQQIQ-SVCMECQGHGERISPKDRCKSCNGRKIVREK
R.G.K...E..CCPNC..TG.QIRIH.Q.G.G.........CMEC.GHGE.ISPKDRCK..NGRKIV..K
RetrocopyRSGEKKRREG*CCPNCQVTGLQIRIH>Q*GLGWFSTLSLCACMECHGHGE*ISPKDRCKHENGRKIV*GK
ParentalKILEVHIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQK
KILEVH.D..MK.GQKITFHGEGD.EPGLEPGDIII.LD.KDHAVFT...ED.FM.MD.QLV..LCGFQK
RetrocopyKILEVHVDNDMKYGQKITFHGEGDKEPGLEPGDIIIELDEKDHAVFT*Q-ED*FMSMDRQLVKILCGFQK
ParentalPISTLDNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKL
PISTLD..TIVITSHPGQ.VK.G.IKCVLNE.MPI..RPYEK..LII.FKVNFPENGFLS.DKLS.L.KL
RetrocopyPISTLDY*TIVITSHPGQTVKYGEIKCVLNEVMPIFHRPYEKHHLIIKFKVNFPENGFLSHDKLS*LGKL
ParentalLPERKEVEETDEMDQV-ELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS
LP.RKE.EE..EMDQV..LV.FD..QE.....NGE..EDD.HHPRGGV.CQTS
RetrocopyLPDRKEIEEIVEMDQV>KLVYFDSDQEKQHYCNGETCEDDKHHPRGGVHCQTS

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 296 .47 RPM
SRP007412_cerebellum 0 .00 RPM 195 .90 RPM
SRP007412_heart 0 .00 RPM 92 .21 RPM
SRP007412_kidney 0 .00 RPM 197 .16 RPM
SRP007412_liver 0 .00 RPM 280 .16 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_2111 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2111 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2111 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2331
Pan troglodytes retro_ptro_1705
Callithrix jacchus retro_cjac_2730
Parental genes homology:
Parental genes homology involve 21 parental genes, and 128 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000075894 retrocopies
retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Bos taurus ENSBTAG000000162656 retrocopies
retro_btau_1440, retro_btau_1599, retro_btau_1800, retro_btau_1826, retro_btau_574, retro_btau_828,
Canis familiaris ENSCAFG0000000181823 retrocopies
retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Callithrix jacchus ENSCJAG0000000802210 retrocopies
retro_cjac_1645, retro_cjac_1777, retro_cjac_2015, retro_cjac_2120, retro_cjac_2730, retro_cjac_2731, retro_cjac_2763, retro_cjac_3037, retro_cjac_3762, retro_cjac_887,
Cavia porcellus ENSCPOG000000004626 retrocopies
retro_cpor_1456, retro_cpor_225, retro_cpor_386, retro_cpor_396, retro_cpor_561, retro_cpor_781,
Dasypus novemcinctus ENSDNOG000000183423 retrocopies
retro_dnov_1139, retro_dnov_640, retro_dnov_884,
Felis catus ENSFCAG000000087295 retrocopies
retro_fcat_1241, retro_fcat_1407, retro_fcat_1502, retro_fcat_1984, retro_fcat_811,
Homo sapiens ENSG000000860614 retrocopies
retro_hsap_2331, retro_hsap_2569, retro_hsap_3647, retro_hsap_4889,
Gorilla gorilla ENSGGOG000000070303 retrocopies
retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Myotis lucifugus ENSMLUG000000160867 retrocopies
retro_mluc_1245, retro_mluc_1485, retro_mluc_1737, retro_mluc_1878, retro_mluc_2062, retro_mluc_2579, retro_mluc_576,
Monodelphis domestica ENSMODG000000033847 retrocopies
retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Mustela putorius furoENSMPUG000000042312 retrocopies
retro_mputfur_1543, retro_mputfur_487,
Nomascus leucogenys ENSNLEG000000052684 retrocopies
retro_nleu_1255, retro_nleu_2550, retro_nleu_2793, retro_nleu_509,
Oryctolagus cuniculus ENSOCUG000000048332 retrocopies
retro_ocun_516, retro_ocun_70,
Pongo abelii ENSPPYG00000019141 4 retrocopies
retro_pabe_1892, retro_pabe_2111 , retro_pabe_2559, retro_pabe_2994,
Pan troglodytes ENSPTRG000000208524 retrocopies
retro_ptro_1499, retro_ptro_1705, retro_ptro_177, retro_ptro_2472,
Rattus norvegicus ENSRNOG000000070292 retrocopies
retro_rnor_2208, retro_rnor_608,
Sarcophilus harrisii ENSSHAG000000123661 retrocopy
retro_shar_762,
Ictidomys tridecemlineatus ENSSTOG000000052004 retrocopies
retro_itri_265, retro_itri_303, retro_itri_378, retro_itri_809,
Tupaia belangeri ENSTBEG0000000059623 retrocopies
retro_tbel_1281, retro_tbel_134, retro_tbel_1529, retro_tbel_1542, retro_tbel_2260, retro_tbel_2293, retro_tbel_2316, retro_tbel_2428, retro_tbel_2445, retro_tbel_2917, retro_tbel_2965, retro_tbel_2972, retro_tbel_329, retro_tbel_3345, retro_tbel_3353, retro_tbel_3692, retro_tbel_4014, retro_tbel_4223, retro_tbel_432, retro_tbel_591, retro_tbel_617, retro_tbel_634, retro_tbel_842,
Tursiops truncatus ENSTTRG000000073874 retrocopies
retro_ttru_1181, retro_ttru_1551, retro_ttru_567, retro_ttru_783,


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