RetrogeneDB ID:

retro_pabe_2978

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:6:89210764..89211804(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTB
Ensembl ID:ENSPPYG00000017336
Aliases:None
Description:Actin, cytoplasmic 1 Actin, cytoplasmic 1, N-terminally processed [Source:UniProtKB/Swiss-Prot;Acc:Q5R6G0]


Retrocopy-Parental alignment summary:






>retro_pabe_2978
GCCCCCCGGGCCGTCTTCCCCTCCATTGTGGGGCACCCCAGGCACCAGGGTGTGATGGTGGGCATGGGTCAGAAGGACTC
CTATGTGGGCAAGGAGGCCCAGAGCAAGAGAGGCATCCTGACTCTCAAGTACCCCATCAAGCATGGCAACGTCACCAACT
GGGACGACATGGAGAAGATCTGGCACCACACCCACAACAAGGTGCGTGTGACTGCCGAGGAGCACCCCGTGCTGCTGACC
GAGGCCCCCCTGAACCCCAAACCCAACCATGAGAAGATGACCCAGTTCATCATGTTTGAGACCTCCAACACCCCAGCCAT
GTATGTGGCCATCCAGGCCGTGCTGTCCCTGTATGCCTCTGGTGGTACCACTGGCATCATGATGCACCCGGTAACAGGGT
CACCCACACTCTGTCCATCTAGGAGGGGTACGCCCTCCCCACGCCATCCTGCGTCTGAACCTGGCTGGCGGGGACCTGAC
TGACTACTTCAAGAAGACCCTCACCCAGCACCGCTACAGCTTCACCACCACACCGAGCGGGAAATCATGTGTGACATCAA
GGAGAAGCTGTGCTACGTCGCCCTGGAATTCGAGCAGGAGATGGCCTCGGTGGCCTCCAGCTCCTCCCTGGAGAAGAGCT
ATGAACTGCCAGACGGCCAGGTCATCACCATCGGCAATGAGCGGTTCCGCTGCCCCGAGGCACTCTTCCAGCCTTCCTTT
CTGGGCATGGAATCCTGTGGCATCCATGACACTACCTTCAACTCCATCATGAAGTGTGACATCCACAAAGACCTGTATGC
CAACACAGTGCTGTCTGGTGGCACCACCATGTACCCTGGCATCACAGACAGGATGCAGAGGAGATCACCAGCCTGGCGCC
CAGCACGATGAAGATCAAGATCATTGCTCCTCCCCAGTGCAAGCGCTCCGTGTGGATTGGCTGCTCCATCCTAGCCTCCA
CTTCCACCTTCCAGCAGATGTGGATCAGCAAGCAGGAGTAGGACTAGTCCAGGGCCTCCATCGTCCACAGCAAATGCTTC

ORF - retro_pabe_2978 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.66 %
Parental protein coverage: 93.33 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELR
APRAVFPSIVG.PRHQGVMVGMGQKDSYVG.EAQSKRGILTLKYPI.HG.VTNWDDMEKIWHHT..N..R
RetrocopyAPRAVFPSIVGHPRHQGVMVGMGQKDSYVGKEAQSKRGILTLKYPIKHGNVTNWDDMEKIWHHT-HNKVR
ParentalVAPEEHPVLLTEAPLNPKANREKMTQ-IMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDS-GDGVTHTV
V..EEHPVLLTEAPLNPK.N.EKMTQ.IMFET.NTPAMYVAIQAVLSLYASG.TTGI.M...G..VTHT.
RetrocopyVTAEEHPVLLTEAPLNPKPNHEKMTQFIMFETSNTPAMYVAIQAVLSLYASGGTTGIMMHP<GNRVTHTL
ParentalPIYEGYALP-HAILRLDLAGRDLTDYLMKILTERGYSFTTT-AEREIVRDIKEKLCYVALDFEQEMATAA
.I.EGYALP.HAILRL.LAG.DLTDY..K.LT...YSFTTT..EREI..DIKEKLCYVAL.FEQEMA..A
RetrocopySI*EGYALP<HAILRLNLAGGDLTDYFKKTLTQHRYSFTTT<TEREIMCDIKEKLCYVALEFEQEMASVA
ParentalSSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSG
SSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIH.TTFNSIMKC..DI.KDLYANTVLSG
RetrocopySSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHDTTFNSIMKC--DIHKDLYANTVLSG
ParentalGTTMYPGIADRMQK-EITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIV
GTTMYPGI.DRMQ..EIT.LAPSTMKIKIIAPP..K.SVWIG.SILAS.STFQQMWISKQE.D.S..SIV
RetrocopyGTTMYPGITDRMQR<EITSLAPSTMKIKIIAPPQCKRSVWIGCSILASTSTFQQMWISKQE*D*SRASIV
ParentalHRKCF
H.KCF
RetrocopyHSKCF

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 .17 RPM 1655 .73 RPM
SRP007412_cerebellum 0 .00 RPM 578 .33 RPM
SRP007412_heart 0 .03 RPM 386 .86 RPM
SRP007412_kidney 0 .13 RPM 1247 .35 RPM
SRP007412_liver 0 .03 RPM 1654 .82 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_2978 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2978 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2978 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3631
Pan troglodytes retro_ptro_2454
Gorilla gorilla retro_ggor_2449
Parental genes homology:
Parental genes homology involve 24 parental genes, and 102 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066011 retrocopy
retro_amel_11,
Cavia porcellus ENSCPOG000000134671 retrocopy
retro_cpor_60,
Homo sapiens ENSG000000756246 retrocopies
retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Gallus gallus ENSGALG000000096211 retrocopy
retro_ggal_4,
Gorilla gorilla ENSGGOG0000000113318 retrocopies
retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292, retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Meleagris gallopavo ENSMGAG000000039602 retrocopies
retro_mgal_5, retro_mgal_6,
Macaca mulatta ENSMMUG000000111531 retrocopy
retro_mmul_135,
Mustela putorius furoENSMPUG000000166122 retrocopies
retro_mputfur_440, retro_mputfur_461,
Mus musculus ENSMUSG000000295807 retrocopies
retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Ornithorhynchus anatinus ENSOANG000000077162 retrocopies
retro_oana_4, retro_oana_8,
Otolemur garnettii ENSOGAG000000083481 retrocopy
retro_ogar_2637,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pongo abelii ENSPPYG000000024591 retrocopy
retro_pabe_3027,
Pongo abelii ENSPPYG000000026051 retrocopy
retro_pabe_1930,
Pongo abelii ENSPPYG000000063181 retrocopy
retro_pabe_1317,
Pongo abelii ENSPPYG0000000873511 retrocopies
retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pongo abelii ENSPPYG00000017336 23 retrocopies
retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978 , retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Rattus norvegicus ENSRNOG0000003425410 retrocopies
retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856, retro_rnor_2978, retro_rnor_351, retro_rnor_459, retro_rnor_935,
Sarcophilus harrisii ENSSHAG000000126944 retrocopies
retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa ENSSSCG000000075851 retrocopy
retro_sscr_548,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Ictidomys tridecemlineatus ENSSTOG000000147973 retrocopies
retro_itri_149, retro_itri_1881, retro_itri_4,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,




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