RetrogeneDB ID:

retro_pabe_3644

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:61981283..61982393(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DKFZP468F2127
Ensembl ID:ENSPPYG00000004562
Aliases:None
Description:keratin, type II cytoskeletal 8 [Source:RefSeq peptide;Acc:NP_001127365]


Retrocopy-Parental alignment summary:






>retro_pabe_3644
GGAGGATATGCTGGGGCCAGTGGTATAGGAGGCATTACAGCTGTCATGGTGAACCAGAGCCTGCTGAGCCCCTTTAAGAT
GGATGTGGACCCCAACATCAAGGCCATGAAAACTCAGTAGAAGGACACCATCAAGACGTTCAACAACAAGTTTTTCTCCT
TCATCATCAAGGTATAGTTCCTGGAGTAGCAGAACAGGATGCTGAAGATGAAGTGAAGCCTCTTGCAGCAGCAGCAGAAG
ACAGCTTGGAGCAACATGAACATGTTCAAGAGCTACATCAACAACCTTTGCAGGCAACTGGAAAGGTTGGAACAAGAGAA
GCTGAAGCTGGAGGCAGAGCTTGGCAATATGCAGGGGCTGGTGGAGGACTTCAGTAATGTGTATGATGATGAGATCAACA
AGGGTGCAGAGATGGAGAATGAATTTGTCCTCTTTAAGAAGAATGTGAATGAAGCTTACATGACCAAGATAGAGCTGGAG
TATCACCTGGAAGGGCTGACTGATGAGATCAGCTTTCTCAGGCAGCTATATAAAGAGGATATCTGCAAGCTGCAGTCCCA
TATCTTTAACATATCTGTGGTTCTGTTCAGGAACAACAGCCACTCCTTGCACATGGACAGCACCATGGCCAAGGGCTGTG
CCCCATATGAGAAGATCATCAACCACAGCTGAGCCAAGGCTAAAAACATGTACCAGATTAAGTATGAGAAGCTGCAGACA
CTGGCTGGGAAGCACAGGGATGATTTGTGTTGAAGAAAGATGGAGATCTCCAAAATGAACCAGAACATCAGCTGGCTCCA
GGCACAGATTGAGGGTCTTAAAGGCCAGAGGGCTTCCTTGGAGGCTGCCATTGTGGATGCAGAGCAGTGTGAAGAGCTGG
TCATTAAGAATGCCTACACCAAGCTGGTGAAACTGGAGGCTGTCTTGCAGTGGGCCAAGCAGGATATGGCATGGGAGCTG
CATAATTATCAGGAACTGATGAGAGTCAATCAAGCCCCGGACATTGAGACTGACACCTACAGGAAACTTCTGGAAGGTGA
ATAGAGCTGCCTGGAGTCTGGAATGCAGAACATGTTTATCCATATGAAGACTACAAGTGGCTATTCAGGT

ORF - retro_pabe_3644 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.16 %
Parental protein coverage: 82.62 %
Number of stop codons detected: 7
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalGGYGG-SGMGGITAVTVNQSL-SPV-LEVDPNI-AVRTQEKEQIKTLNNKFASFIDKVRFLEQQNKMLET
GGY.G.SG.GGITAV.VNQSL.SP....VDPNI.A..TQ.K..IKT.NNKF.SFI.KV.FLE.QN.ML..
RetrocopyGGYAGASGIGGITAVMVNQSLLSPFKMDVDPNIKAMKTQ*KDTIKTFNNKFFSFIIKV*FLE*QNRMLKM
ParentalKWSLLQQQ-KTARSNMDNMFESYINNLRRQLETLGQEKLKLEAELGNMQGLVEDFKNKYEDEINKRTEME
K.SLLQQQ.KTA.SNM.NMF.SYINNL.RQLE.L.QEKLKLEAELGNMQGLVEDF.N.Y.DEINK..EME
RetrocopyK*SLLQQQQKTAWSNM-NMFKSYINNLCRQLERLEQEKLKLEAELGNMQGLVEDFSNVYDDEINKGAEME
ParentalNEFVLIKKDVDEAYMNKVELESRLEGLTDEINFLRQLYEEEIRELQSQISDTSVVLSMDNSRSLDMDSII
NEFVL.KK.V.EAYM.K.ELE..LEGLTDEI.FLRQLY.E.I..LQS.I...SVVL...NS.SL.MDS..
RetrocopyNEFVLFKKNVNEAYMTKIELEYHLEGLTDEISFLRQLYKEDICKLQSHIFNISVVLFRNNSHSLHMDSTM
ParentalAEVKAQYEDIANRSRAEAESMYQIKYEELQSLAGKHGDDLRRTKTEISEMNRNISRLQAEIEGLKGQRAS
A...A.YE.I.N.S.A.A..MYQIKYE.LQ.LAGKH.DDL...K.EIS.MN.NIS.LQA.IEGLKGQRAS
RetrocopyAKGCAPYEKIINHS*AKAKNMYQIKYEKLQTLAGKHRDDLC*RKMEISKMNQNISWLQAQIEGLKGQRAS
ParentalLEAAIADAEQRGELAIKDANAKLSELEAALQRAKQDMARQLREYQELMNVKLALDIEIATYRKLLEGEES
LEAAI.DAEQ..EL.IK.A..KL..LEA.LQ.AKQDMA..L..YQELM.V..A.DIE..TYRKLLEGE.S
RetrocopyLEAAIVDAEQCEELVIKNAYTKLVKLEAVLQWAKQDMAWELHNYQELMRVNQAPDIETDTYRKLLEGE*S
ParentalRLESGMQNMSIHTKTTSGYAG
.LESGMQNM.IH.KTTSGY.G
RetrocopyCLESGMQNMFIHMKTTSGYSG

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 .55 RPM
SRP007412_cerebellum 0 .00 RPM 0 .12 RPM
SRP007412_heart 0 .00 RPM 23 .57 RPM
SRP007412_kidney 0 .00 RPM 106 .83 RPM
SRP007412_liver 0 .00 RPM 163 .17 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_3644 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3644 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3644 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4691
Gorilla gorilla retro_ggor_2918
Parental genes homology:
Parental genes homology involve 17 parental genes, and 152 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000071992 retrocopies
retro_cfam_1036, retro_cfam_1590,
Callithrix jacchus ENSCJAG000000181473 retrocopies
retro_cjac_124, retro_cjac_167, retro_cjac_216,
Cavia porcellus ENSCPOG000000026155 retrocopies
retro_cpor_1269, retro_cpor_1459, retro_cpor_233, retro_cpor_302, retro_cpor_516,
Dasypus novemcinctus ENSDNOG000000074003 retrocopies
retro_dnov_1267, retro_dnov_1886, retro_dnov_2358,
Felis catus ENSFCAG000000002982 retrocopies
retro_fcat_1142, retro_fcat_891,
Homo sapiens ENSG0000017042128 retrocopies
retro_hsap_1012, retro_hsap_1024, retro_hsap_1324, retro_hsap_1513, retro_hsap_1557, retro_hsap_1599, retro_hsap_169, retro_hsap_1708, retro_hsap_235, retro_hsap_2354, retro_hsap_2669, retro_hsap_2731, retro_hsap_2768, retro_hsap_2797, retro_hsap_2842, retro_hsap_3069, retro_hsap_3359, retro_hsap_3379, retro_hsap_3433, retro_hsap_371, retro_hsap_3963, retro_hsap_4203, retro_hsap_4688, retro_hsap_4691, retro_hsap_4775, retro_hsap_644, retro_hsap_844, retro_hsap_932,
Gorilla gorilla ENSGGOG0000001467318 retrocopies
retro_ggor_1160, retro_ggor_1787, retro_ggor_1862, retro_ggor_1897, retro_ggor_1900, retro_ggor_2320, retro_ggor_2662, retro_ggor_2913, retro_ggor_2918, retro_ggor_297, retro_ggor_2975, retro_ggor_382, retro_ggor_564, retro_ggor_66, retro_ggor_691, retro_ggor_751, retro_ggor_803, retro_ggor_809,
Macaca mulatta ENSMMUG0000000216322 retrocopies
retro_mmul_1069, retro_mmul_1122, retro_mmul_1178, retro_mmul_1349, retro_mmul_1351, retro_mmul_1412, retro_mmul_1697, retro_mmul_1753, retro_mmul_1810, retro_mmul_1855, retro_mmul_1866, retro_mmul_2097, retro_mmul_2137, retro_mmul_2357, retro_mmul_2431, retro_mmul_2546, retro_mmul_289, retro_mmul_488, retro_mmul_58, retro_mmul_766, retro_mmul_816, retro_mmul_886,
Mustela putorius furoENSMPUG000000064417 retrocopies
retro_mputfur_1101, retro_mputfur_1208, retro_mputfur_1271, retro_mputfur_1557, retro_mputfur_1587, retro_mputfur_556, retro_mputfur_895,
Mus musculus ENSMUSG000000493821 retrocopy
retro_mmus_2905,
Nomascus leucogenys ENSNLEG000000177338 retrocopies
retro_nleu_1913, retro_nleu_225, retro_nleu_2285, retro_nleu_2421, retro_nleu_2485, retro_nleu_2727, retro_nleu_2787, retro_nleu_672,
Oryctolagus cuniculus ENSOCUG000000069451 retrocopy
retro_ocun_313,
Otolemur garnettii ENSOGAG0000001174016 retrocopies
retro_ogar_1076, retro_ogar_1162, retro_ogar_1256, retro_ogar_1572, retro_ogar_1874, retro_ogar_1898, retro_ogar_1952, retro_ogar_2004, retro_ogar_2149, retro_ogar_2177, retro_ogar_2261, retro_ogar_2500, retro_ogar_3198, retro_ogar_3318, retro_ogar_339, retro_ogar_664,
Pongo abelii ENSPPYG000000045481 retrocopy
retro_pabe_1103,
Pongo abelii ENSPPYG00000004562 31 retrocopies
retro_pabe_1102, retro_pabe_1261, retro_pabe_1289, retro_pabe_1460, retro_pabe_1743, retro_pabe_2063, retro_pabe_2077, retro_pabe_2129, retro_pabe_2142, retro_pabe_2214, retro_pabe_2270, retro_pabe_2352, retro_pabe_2544, retro_pabe_2741, retro_pabe_2763, retro_pabe_2787, retro_pabe_2842, retro_pabe_2926, retro_pabe_2943, retro_pabe_3138, retro_pabe_332, retro_pabe_3439, retro_pabe_3644 , retro_pabe_3716, retro_pabe_417, retro_pabe_460, retro_pabe_569, retro_pabe_605, retro_pabe_701, retro_pabe_803, retro_pabe_851,
Pteropus vampyrus ENSPVAG000000093603 retrocopies
retro_pvam_1299, retro_pvam_1396, retro_pvam_45,
Rattus norvegicus ENSRNOG000000097791 retrocopy
retro_rnor_807,


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