RetrogeneDB ID:

retro_ptro_1009

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:15:41475177..41475790(+)
Located in intron of:ENSPTRG00000007010
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GAPDH
Ensembl ID:ENSPTRG00000004577
Aliases:GAPDH, GAPD
Description:glyceraldehyde-3-phosphate dehydrogenase [Source:HGNC Symbol;Acc:4141]


Retrocopy-Parental alignment summary:






>retro_ptro_1009
TTGATGGGCATGAACCATGAGAAGTATGAAAGCAACCTCACAATCATCAGCATTGCCTCCTGCACCACCAACTGCTTAGC
ATTCTCTGACCAAGATCATCCATGACAGCTCTGGCATCATGGAGGGACTCATGACCACAGTCCCTGCTATCACTGCCACC
CAGGAGACCTATGGATGGCTTTTCTGGGAAACTGTGACGTCATGGTTGTAGGGCTCTGCAGAACATTATTCCTGCATCTA
CTGGAACTTCCACGGCTGTGGGCAAGGACATCCCCGAGCTGAATGGGGAGATCACTGGCATGGCCTTCCTCGTCCCTACC
ACCAATGTGTCAGTTGTGGACCTGACCTGCTGTCTGGAGTAACCTGCCAAATATGATGGCTTCAAGAAGATGGTGAAGCA
GGCATCGGAAGGCCCTTCAAGGGCACACTGGGCTACACTGAACACCAAGTTGTCCCCTGTGACTTTAACGGTGACACTCC
CTCTTCCACTTTTAATTCTGGGGCTAGCATTGCCCTCAGCAACCATTTTGTCAAGTTAATTTCCTGGTATGACAATTAGT
TTTGCTACAGCAATGGGGTGGTGGACCTCATGGTCCACATGGCCTCCAAGGAA

ORF - retro_ptro_1009 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.88 %
Parental protein coverage: 60.9 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalVMGVNHEKYDNSLKIISNASCTTNCLA-PLAKVIHDNFGIVEGLMTTVHAITATQKT-VDGPSGKLWRDG
.MG.NHEKY...L.IIS.ASCTTNCLA..L.K.IHD..GI.EGLMTTV.AITATQ.T..DG.SGKL.R.G
RetrocopyLMGMNHEKYESNLTIISIASCTTNCLA>SLTKIIHDSSGIMEGLMTTVPAITATQET>MDGFSGKL*RHG
ParentalRGALQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQASEG-
..ALQNIIPASTG...AVGK.IPELNG..TGMAF.VPT.NVSVVDLTC.LE.PAKYD..KK.VKQASEG.
RetrocopyCRALQNIIPASTGTSTAVGKDIPELNGEITGMAFLVPTTNVSVVDLTCCLE*PAKYDGFKKMVKQASEG<
ParentalPLKGILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMAHMASKE
P.KG.LGYTEHQVV..DFN.DT.SSTF..GA.IAL..HFVKLISWYDN.F.YSN.VVDLM.HMASKE
RetrocopyPFKGTLGYTEHQVVPCDFNGDTPSSTFNSGASIALSNHFVKLISWYDN*FCYSNGVVDLMVHMASKE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .52 RPM 2168 .65 RPM
SRP007412_cerebellum 0 .61 RPM 1166 .58 RPM
SRP007412_heart 0 .12 RPM 1898 .41 RPM
SRP007412_kidney 0 .71 RPM 1211 .09 RPM
SRP007412_liver 0 .13 RPM 1233 .46 RPM
SRP007412_testis 0 .21 RPM 203 .39 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1009 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1009 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1009 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1490
Gorilla gorilla retro_ggor_1143
Pongo abelii retro_pabe_1239
Macaca mulatta retro_mmul_2134

Parental genes homology:
Parental genes homology involve 21 parental genes, and 510 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066755 retrocopies
Ailuropoda melanoleuca ENSAMEG0000001432935 retrocopies
Canis familiaris ENSCAFG000000150774 retrocopies
Cavia porcellus ENSCPOG000000263501 retrocopy
Erinaceus europaeus ENSEEUG000000114443 retrocopies
Homo sapiens ENSG0000011164042 retrocopies
Gorilla gorilla ENSGGOG0000000955330 retrocopies
Loxodonta africana ENSLAFG000000027803 retrocopies
Macropus eugenii ENSMEUG0000001527367 retrocopies
Microcebus murinus ENSMICG0000000654616 retrocopies
Macaca mulatta ENSMMUG0000001867933 retrocopies
Monodelphis domestica ENSMODG0000001806641 retrocopies
Mustela putorius furoENSMPUG0000001689128 retrocopies
Mus musculus ENSMUSG00000057666109 retrocopies
retro_mmus_1029, retro_mmus_1082, retro_mmus_1136, retro_mmus_1193, retro_mmus_1249, retro_mmus_1319, retro_mmus_1328, retro_mmus_136, retro_mmus_1365, retro_mmus_1371, retro_mmus_1467, retro_mmus_1474, retro_mmus_1480, retro_mmus_1615, retro_mmus_1692, retro_mmus_1721, retro_mmus_1728, retro_mmus_1886, retro_mmus_1922, retro_mmus_1957, retro_mmus_1983, retro_mmus_1985, retro_mmus_2009, retro_mmus_2020, retro_mmus_2030, retro_mmus_2100, retro_mmus_211, retro_mmus_2119, retro_mmus_2122, retro_mmus_2148, retro_mmus_2158, retro_mmus_2175, retro_mmus_2206, retro_mmus_2216, retro_mmus_2248, retro_mmus_2298, retro_mmus_2370, retro_mmus_2371, retro_mmus_2389, retro_mmus_2463, retro_mmus_2477, retro_mmus_2481, retro_mmus_2512, retro_mmus_2556, retro_mmus_2587, retro_mmus_2623, retro_mmus_2626, retro_mmus_2647, retro_mmus_2681, retro_mmus_2755, retro_mmus_2761, retro_mmus_2764, retro_mmus_2848, retro_mmus_2872, retro_mmus_2911, retro_mmus_2912, retro_mmus_2913, retro_mmus_2914, retro_mmus_2915, retro_mmus_2920, retro_mmus_2932, retro_mmus_2943, retro_mmus_300, retro_mmus_3036, retro_mmus_3064, retro_mmus_3120, retro_mmus_3137, retro_mmus_3140, retro_mmus_3148, retro_mmus_3151, retro_mmus_3188, retro_mmus_3193, retro_mmus_3197, retro_mmus_3216, retro_mmus_3228, retro_mmus_3306, retro_mmus_3335, retro_mmus_3336, retro_mmus_3357, retro_mmus_3377, retro_mmus_3445, retro_mmus_3514, retro_mmus_3575, retro_mmus_3650, retro_mmus_3658, retro_mmus_3693, retro_mmus_3716, retro_mmus_3814, retro_mmus_416, retro_mmus_437, retro_mmus_48, retro_mmus_553, retro_mmus_608, retro_mmus_619, retro_mmus_628, retro_mmus_635, retro_mmus_698, retro_mmus_745, retro_mmus_765, retro_mmus_766, retro_mmus_787, retro_mmus_811, retro_mmus_893, retro_mmus_914, retro_mmus_921, retro_mmus_946, retro_mmus_952, retro_mmus_976, retro_mmus_996,
Pongo abelii ENSPPYG0000000418938 retrocopies
Pan troglodytes ENSPTRG00000004577 43 retrocopies
Pan troglodytes ENSPTRG000000108481 retrocopy
Rattus norvegicus ENSRNOG000000186304 retrocopies
Rattus norvegicus ENSRNOG000000306382 retrocopies
Sarcophilus harrisii ENSSHAG000000149534 retrocopies
Xenopus tropicalis ENSXETG000000339751 retrocopy



Copyright © RetrogeneDB 2014-2017