RetrogeneDB ID:

retro_pabe_3405

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:9:45832543..45833014(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000025842
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSPPYG00000019622
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_pabe_3405
GAGATCAAAGTCGTATATCTGAGGTGCACCAGAGGTGAAGTCGGTGCCACTTCTGCCCTGGCCCCCAAGATCGGTCCCCT
GGGTCTGTCTCCAAAAAAGGTTGGTGATGACATTGCCGAGGCAACGGGTGACTGGAAGGGCCTGAGGATTACAGTGAAAC
TGACCATTCAGAACAGACAGGCCCAGATTGAGGTGGTGCCTTCTGCCTCTGCCCTGATGATCAAAGCCCTCAAGGAACCA
CCAAGAGACAGAAAGAAACAGAAAAACATTAAACACAGTGGGAATATCACTTTTGATGAGATCGTCAACATTGCTCGACA
GATGCGGCACCGATCCTTAGCCAGAGAACTCTCTGGAACCATTAAAGAGATCCTGGGGACTGCCCAGTCTGTGGGCTGTA
ATGTTGATGGCCGCCACCCTCATGACATCATAGATGACATCAATAGTGGTGCTGTGGAATGCCCAGCCAGT

ORF - retro_pabe_3405 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.09 %
Parental protein coverage: 68.86 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQIEVVPSAS
EIKVVYLRCT.GEVGATSALAPKIGPLGLSPKKVGDDIA.ATGDWKGLRITVKLTIQNRQAQIEVVPSAS
RetrocopyEIKVVYLRCTRGEVGATSALAPKIGPLGLSPKKVGDDIAEATGDWKGLRITVKLTIQNRQAQIEVVPSAS
ParentalALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVGCNVDGRHP
AL.IKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVGCNVDGRHP
RetrocopyALMIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVGCNVDGRHP
ParentalHDIIDDINSGAVECPAS
HDIIDDINSGAVECPAS
RetrocopyHDIIDDINSGAVECPAS

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 .00 RPM 80 .56 RPM
SRP007412_cerebellum 0 .00 RPM 46 .21 RPM
SRP007412_heart 0 .00 RPM 94 .65 RPM
SRP007412_kidney 0 .03 RPM 193 .41 RPM
SRP007412_liver 0 .03 RPM 195 .27 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3405 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3405 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3405 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 19 parental genes, and 369 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000069633 retrocopies
Callithrix jacchus ENSCJAG000000180821 retrocopy
Homo sapiens ENSG0000019795841 retrocopies
Gorilla gorilla ENSGGOG0000000064834 retrocopies
Latimeria chalumnae ENSLACG000000153733 retrocopies
Macropus eugenii ENSMEUG0000000738012 retrocopies
Macaca mulatta ENSMMUG000000004222 retrocopies
Monodelphis domestica ENSMODG000000045719 retrocopies
Mus musculus ENSMUSG000000389001 retrocopy
Oryctolagus cuniculus ENSOCUG000000049029 retrocopies
Otolemur garnettii ENSOGAG00000000597120 retrocopies
retro_ogar_1002, retro_ogar_1010, retro_ogar_1049, retro_ogar_1069, retro_ogar_1106, retro_ogar_1117, retro_ogar_1137, retro_ogar_1140, retro_ogar_1181, retro_ogar_1188, retro_ogar_1189, retro_ogar_1192, retro_ogar_1230, retro_ogar_1247, retro_ogar_1263, retro_ogar_1295, retro_ogar_1331, retro_ogar_1341, retro_ogar_1408, retro_ogar_1409, retro_ogar_1427, retro_ogar_1457, retro_ogar_1464, retro_ogar_1489, retro_ogar_1503, retro_ogar_1534, retro_ogar_1536, retro_ogar_1550, retro_ogar_1569, retro_ogar_1570, retro_ogar_1579, retro_ogar_1606, retro_ogar_1621, retro_ogar_1709, retro_ogar_1717, retro_ogar_1739, retro_ogar_1789, retro_ogar_1803, retro_ogar_1810, retro_ogar_1825, retro_ogar_1836, retro_ogar_1881, retro_ogar_1885, retro_ogar_1916, retro_ogar_1923, retro_ogar_1937, retro_ogar_1941, retro_ogar_1948, retro_ogar_1969, retro_ogar_1975, retro_ogar_1987, retro_ogar_2055, retro_ogar_2115, retro_ogar_2134, retro_ogar_2172, retro_ogar_2179, retro_ogar_2180, retro_ogar_2208, retro_ogar_2209, retro_ogar_2230, retro_ogar_2291, retro_ogar_2323, retro_ogar_2387, retro_ogar_2483, retro_ogar_2495, retro_ogar_2511, retro_ogar_2570, retro_ogar_2620, retro_ogar_2622, retro_ogar_2624, retro_ogar_2749, retro_ogar_2768, retro_ogar_2809, retro_ogar_2904, retro_ogar_2935, retro_ogar_2945, retro_ogar_2953, retro_ogar_2980, retro_ogar_3004, retro_ogar_3017, retro_ogar_303, retro_ogar_3035, retro_ogar_3128, retro_ogar_3135, retro_ogar_3164, retro_ogar_3394, retro_ogar_3489, retro_ogar_395, retro_ogar_398, retro_ogar_412, retro_ogar_427, retro_ogar_452, retro_ogar_480, retro_ogar_512, retro_ogar_513, retro_ogar_538, retro_ogar_560, retro_ogar_587, retro_ogar_624, retro_ogar_636, retro_ogar_653, retro_ogar_655, retro_ogar_667, retro_ogar_668, retro_ogar_669, retro_ogar_683, retro_ogar_700, retro_ogar_734, retro_ogar_737, retro_ogar_744, retro_ogar_747, retro_ogar_775, retro_ogar_818, retro_ogar_853, retro_ogar_868, retro_ogar_901, retro_ogar_927, retro_ogar_956, retro_ogar_962, retro_ogar_964,
Ochotona princeps ENSOPRG0000001107821 retrocopies
Pongo abelii ENSPPYG00000019622 44 retrocopies
Pan troglodytes ENSPTRG000000228081 retrocopy
Pteropus vampyrus ENSPVAG0000000092515 retrocopies
Rattus norvegicus ENSRNOG000000162204 retrocopies
Sarcophilus harrisii ENSSHAG000000178648 retrocopies
Sus scrofa ENSSSCG0000000561214 retrocopies
Vicugna pacos ENSVPAG0000000512327 retrocopies



Copyright © RetrogeneDB 2014-2017