RetrogeneDB ID: | retro_pabe_3190 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 7:140902054..140903563(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KPNB1 | ||
| Ensembl ID: | ENSPPYG00000025935 | ||
| Aliases: | None | ||
| Description: | karyopherin (importin) beta 1 [Source:HGNC Symbol;Acc:6400] |
Retrocopy-Parental alignment summary:
>retro_pabe_3190
GAAATGGATTTGGCAGCAGAACAAGGACGGCCCCCTGAGCACACCAGCAAGTTTTATGCCAAGGGAGCACTACAGTATCT
GGTTCCAATCCTCATACAGACACTAACTAAACAGGATGAAAATGATGATGACGATGACTGGAACCCCTGCAAAGCAGCAG
GGGTGTGCCTCATGCTTCTGGCCACCTGCTGTGAAGATGACATTGTCCCACATGTCCTCCCCTTCATTAAAGAACACATC
AAGAACCCAGACTGGCGGTACCGGGATGCAGCAGTGATGGCTTTTGGTTGTATCTTGGAACGACCAGAGCCCAGTTAGCT
CAAACCACTAGTTATACAGGCTATGCCCACCCTAATAGAATTAATGAAAGACCCCAGTGTAGTTGTTCGAGATACAGCTG
CATGGACTGTAGGCAGAATTTGTGAGCTGCTTCCTGAAGCTGCCATCAATGATGTCTACTTGGCTCTCCTGCTACAGTGT
CTGATTGAGGGTCTCAGTGCTGAACCCAGAGTGGCTTCAAATGTGTGCTGGGCTTTCTCCAGTCTGGCTGAAGCTGCTTA
TGAAGCTGCAGACATTGCTGATGATCAGGAAGAACCAGCTACTTACTGCTTGTCTTCTTCATTTGAACTTATAGTTCAGA
AGCTCCTAGAGACTACAGACAGACCTGATGGACATCAGAACAACCTGAGGAGTTCTGCATATGAATCTCTGATGGAAATT
GTGAAAAACAGTGCCAAGGATTGTTATCCTGCTGTCCAGAAAACGACTTTGGTCATCATGGAACGACTGCAACAGGTTCT
TCAGATGGAGTCACATATCCAGAGCACATCCGATAGAATCCAGTTCAATGACCTTCAGTCTTTACTCTGTGCAACTCTTC
AGAATGTTCTTCGGAAAGTGCAACATCAAGATGCTTTGCAGATCTCTGATGTGGTTATGGCCTCCCTGTTAAGGATGTTC
CAAAGCACAGCTGGGTCTGGGGGAGTACAAGAAGATGCCCTGATGGCAGTTAGCACACTGGTGGAAGTGTTGGGTGGTGA
ATTCCTCAAGTACATGGAGGCCTTTAAACCCTTCCTGGGCATTGGATTAAGAAATTATGCTCAGTACCAGGTTTGTTTGG
CAGCTGTGGGCTTAGTGGGAGACTTGTGCCGTGCCCTGCAATCCAACATCATACCTTTCTGTGACGAGGTGATGCAGCTG
CTTCTGGAAAATTTGGGGAATGAGAACGTCCACAGGTCTGTGAAGCCGCAGATTCTGTCAGTGTTTGGTGATATTGCCCT
TGCTATTGGTGGAGAGTTTAAAAAATACTTAGAGGTTGTATTGAATACTCTTCAGCAGGCCTCCCAAGCCCAGGTGGACA
AGTCAGACTATGACATCATGGATTATCTGAATGAGCTAAGGGAAAGCTGCTTGGAAGCCTATACCGGAATCGTCCAGGGA
TTAAAGGGGGATCGGGAGAACGTACACCCGGATGTGATGCTGGTACAACCCAGAGTAGAATTTATTCTC
ORF - retro_pabe_3190 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.42 % |
| Parental protein coverage: | 68.81 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EASEAAEQGRPPEHTSKFYAKGALQYLVPILTQTLTKQDENDDDDDWNPCKAAGVCLMLLATCCEDDIVP |
| E...AAEQGRPPEHTSKFYAKGALQYLVPIL.QTLTKQDENDDDDDWNPCKAAGVCLMLLATCCEDDIVP | |
| Retrocopy | EMDLAAEQGRPPEHTSKFYAKGALQYLVPILIQTLTKQDENDDDDDWNPCKAAGVCLMLLATCCEDDIVP |
| Parental | HVLPFIKEHIKNPDWRYRDAAVMAFGCILEGPEPSQLKPLVIQAMPTLIELMKDPSVVVRDTAAWTVGRI |
| HVLPFIKEHIKNPDWRYRDAAVMAFGCILE.PEPS.LKPLVIQAMPTLIELMKDPSVVVRDTAAWTVGRI | |
| Retrocopy | HVLPFIKEHIKNPDWRYRDAAVMAFGCILERPEPS*LKPLVIQAMPTLIELMKDPSVVVRDTAAWTVGRI |
| Parental | CELLPEAAINDVYLAPLLQCLIEGLSAEPRVASNVCWAFSSLAEAAYEAADVADDQEEPATYCLSSSFEL |
| CELLPEAAINDVYLA.LLQCLIEGLSAEPRVASNVCWAFSSLAEAAYEAAD.ADDQEEPATYCLSSSFEL | |
| Retrocopy | CELLPEAAINDVYLALLLQCLIEGLSAEPRVASNVCWAFSSLAEAAYEAADIADDQEEPATYCLSSSFEL |
| Parental | IVQKLLETTDRPDGHQNNLRSSAYESLMEIVKNSAKDCYPAVQKTTLVIMERLQQVLQMESHIQSTSDRI |
| IVQKLLETTDRPDGHQNNLRSSAYESLMEIVKNSAKDCYPAVQKTTLVIMERLQQVLQMESHIQSTSDRI | |
| Retrocopy | IVQKLLETTDRPDGHQNNLRSSAYESLMEIVKNSAKDCYPAVQKTTLVIMERLQQVLQMESHIQSTSDRI |
| Parental | QFNDLQSLLCATLQNVLRKVQHQDALQISDVVMASLLRMFQSTAGSGGVQEDALMAVSTLVEVLGGEFLK |
| QFNDLQSLLCATLQNVLRKVQHQDALQISDVVMASLLRMFQSTAGSGGVQEDALMAVSTLVEVLGGEFLK | |
| Retrocopy | QFNDLQSLLCATLQNVLRKVQHQDALQISDVVMASLLRMFQSTAGSGGVQEDALMAVSTLVEVLGGEFLK |
| Parental | YMEAFKPFLGIGLKNYAEYQVCLAAVGLVGDLCRALQSNIIPFCDEVMQLLLENLGNENVHRSVKPQILS |
| YMEAFKPFLGIGL.NYA.YQVCLAAVGLVGDLCRALQSNIIPFCDEVMQLLLENLGNENVHRSVKPQILS | |
| Retrocopy | YMEAFKPFLGIGLRNYAQYQVCLAAVGLVGDLCRALQSNIIPFCDEVMQLLLENLGNENVHRSVKPQILS |
| Parental | VFGDIALAIGGEFKKYLEVVLNTLQQASQAQVDKSDYDMVDYLNELRESCLEAYTGIVQGLKGDQENVHP |
| VFGDIALAIGGEFKKYLEVVLNTLQQASQAQVDKSDYD..DYLNELRESCLEAYTGIVQGLKGD.ENVHP | |
| Retrocopy | VFGDIALAIGGEFKKYLEVVLNTLQQASQAQVDKSDYDIMDYLNELRESCLEAYTGIVQGLKGDRENVHP |
| Parental | DVMLVQPRVEFIL |
| DVMLVQPRVEFIL | |
| Retrocopy | DVMLVQPRVEFIL |
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 .33 RPM | 108 .20 RPM |
| SRP007412_cerebellum | 0 .36 RPM | 87 .67 RPM |
| SRP007412_heart | 0 .15 RPM | 58 .79 RPM |
| SRP007412_kidney | 0 .17 RPM | 91 .85 RPM |
| SRP007412_liver | 0 .03 RPM | 51 .84 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3190 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3190 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3190 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000025935 | 1 retrocopy |
retro_pabe_3190 ,
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