RetrogeneDB ID: | retro_pabe_1836 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 20_random:4456651..4458102(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KLF4 | ||
| Ensembl ID: | ENSPPYG00000019478 | ||
| Aliases: | None | ||
| Description: | Kruppel-like factor 4 (gut) [Source:HGNC Symbol;Acc:6348] |
Retrocopy-Parental alignment summary:
>retro_pabe_1836
ATGAGGCAGCCACCTGGCGAGTCTGACATGGCTGTCAGCGACGCGCTGCTCCCATCTTTCTCCACGTTCGCGTCTGGCCC
GGCGGGAAGGGAGAAGACACTGCATCAGGCAGGTACCCCGAATAACCGCTGGCGGGAGGAGCTCTCCCACATGGAGCGAC
TTCCCCCGGTGCTTCCCGGCCGCCCCTATGACCTGGCGGCGGCGACCGTGGCCACAGACCTGGAGAGCGGCGGAGCCGGT
GCGGCTTGCGGCGGTAGCAACCTGGCGCCCCTACCTCGGAGAGAGACCGAGGAGTTCAACGATCTCCTGGACCTGGACTT
TCATCCTCTCCAATTCGCTGACCCATCCTCCGGAGTCAGTGGCCGCCACCGTGTCCTCGTCAGCGTCAGCCTCCTCCTCC
TCCTCGTCGTCCCCGTCGAGCAGCGGCCCTGCCAGCGCGCCCCCCACCTGCAGCTTCACCGATCCCATCCGGGCCGGGAA
ACACCCGGGCGTGGCGCCGGGAGGCACGGGCGGAGGCCTCTTGATGGCAGGGAGTCCGCTCCCCCTCCGACGGCTCCCTT
CAACCTGGCGGACATCAACGACGTGAGCCCCTCGGGCGGCTTCGTGGCCGAGCTCCTGCGGCCAGAATTGGACCCGGTGT
ACATTCCGCCGCAGCAGCCGCAGCCGCCAGGTGCCGGGCTGATGGGCAAGTTCGTGCTGAAGGCGTCGCTGAGCGCCCCT
GGCAGCGAGTGTGCCCGCCCGTCGGTCATCAGCGTCAGCAAAGGCAGCCCTGACGGCAGCCACCCGGTGGTGGTGGCGCC
CTACAAAGGCGGGCCGCCGCGCACATGCCCCAAGATCAAGCGGGAGGCGGTCTCCTCGTGCACTCACTTGGGCGTTGGAC
CCCCTCTCAGCAATGGCCACCGGCCGGCTGCACACGACTTCCCCCTGGGGCGGCAGCTCCCCAGCAGGACTACCCCGACC
CTGGGTCTGGAGGAAGTGCTGAGCAGCCGGGACTGTCACCCTGCCCTGCCGCTTCCCCCCTCCCCCTCCGGCTTCCATCC
CCACCCGGGGCCCAATTACCCATCCTTCCTGCCCGACCAGATGCAGCCGCAAGTCCCGCCGCTCCATTACCAAGAGCTCA
TGCCACCCGGTTCCTGCATGCCGGAGGAGCCCAAGCCAAAGAGGGGAAGACGATCGTGGCCCCGAAAAGGGCCGCCACCC
ACACTTGTGATTACGCGGGCTGCGGCCAAGCCTACACAAAGAGTTCCCATCTCAAGGCACACCTGCGAACCCACACAGGT
GAGAAACCTTACCACTGTGTCTGGGACAGCTGTGGATGGAAATTCGCCCGCTCGGATGAACTGACCAGGCACTACCGTAA
ACACACTGGGCACCGCCCATTCCAGTGCCAAAAATGCGACCGAGCATTTTCCAGGTCGGACCACCTCGCCTTACACATGA
AGAGGCATTTT
ORF - retro_pabe_1836 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.05 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MRQPPGESDMAVSDALLPSFSTFASGPAGREKTLRQAGAPNNRWREELSHMKRLPPVLPGRPYDLAAATV |
| MRQPPGESDMAVSDALLPSFSTFASGPAGREKTL.QAG.PNNRWREELSHM.RLPPVLPGRPYDLAAATV | |
| Retrocopy | MRQPPGESDMAVSDALLPSFSTFASGPAGREKTLHQAGTPNNRWREELSHMERLPPVLPGRPYDLAAATV |
| Parental | ATDLESGGAGAACGGSNLVPLPRRETEEFNDLLDLDF-ILSNSLTHPPESVAATVSSSASASSSSS--PS |
| ATDLESGGAGAACGGSNL.PLPRRETEEFNDLLDLDF.ILSNSLTHPPESVAATVSSSASASSSSS..PS | |
| Retrocopy | ATDLESGGAGAACGGSNLAPLPRRETEEFNDLLDLDF>ILSNSLTHPPESVAATVSSSASASSSSSSSPS |
| Parental | SSGPASAPSTCSFTYPIRAGNDPGVAPGGTGGGLLY-GRESAPPPTAPFNLADINDVSPSGGFVAELLRP |
| SSGPASAP.TCSFT.PIRAG..PGVAPGGTGGGLL..GRESAPPPTAPFNLADINDVSPSGGFVAELLRP | |
| Retrocopy | SSGPASAPPTCSFTDPIRAGKHPGVAPGGTGGGLLM<GRESAPPPTAPFNLADINDVSPSGGFVAELLRP |
| Parental | ELDPVYIPPQQPQPPGGGLMGKFVLKASLSAPGSEYGSPSVISVSKGSPDGSHPVVVAPYNGGPPRTCPK |
| ELDPVYIPPQQPQPPG.GLMGKFVLKASLSAPGSE...PSVISVSKGSPDGSHPVVVAPY.GGPPRTCPK | |
| Retrocopy | ELDPVYIPPQQPQPPGAGLMGKFVLKASLSAPGSECARPSVISVSKGSPDGSHPVVVAPYKGGPPRTCPK |
| Parental | IKQEAVSSCTHLGAGPPLSNGHRPAAHDFPLGRQLPSRTTPTLGLEEVLSSRDCHPALPLPP---GFHPH |
| IK.EAVSSCTHLG.GPPLSNGHRPAAHDFPLGRQLPSRTTPTLGLEEVLSSRDCHPALPLPP...GFHPH | |
| Retrocopy | IKREAVSSCTHLGVGPPLSNGHRPAAHDFPLGRQLPSRTTPTLGLEEVLSSRDCHPALPLPPSPSGFHPH |
| Parental | PGPNYPSFLPDQMQPQVPPLHYQELMPPGSCMPEEPKPKRGRRSWPR-KRTATHTCDYAGCGKTYTKSSH |
| PGPNYPSFLPDQMQPQVPPLHYQELMPPGSCMPEEPKPKRGRRSWPR.KR.ATHTCDYAGCG..YTKSSH | |
| Retrocopy | PGPNYPSFLPDQMQPQVPPLHYQELMPPGSCMPEEPKPKRGRRSWPR<KRAATHTCDYAGCGQAYTKSSH |
| Parental | LKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYRKHTGHRPFQCQKCDRAFSRSDHLALHMKRHF |
| LKAHLRTHTGEKPYHC.WD.CGWKFARSDELTRHYRKHTGHRPFQCQKCDRAFSRSDHLALHMKRHF | |
| Retrocopy | LKAHLRTHTGEKPYHCVWDSCGWKFARSDELTRHYRKHTGHRPFQCQKCDRAFSRSDHLALHMKRHF |
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 | 1 .38 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .85 RPM |
| SRP007412_heart | 0 .00 RPM | 3 .76 RPM |
| SRP007412_kidney | 0 .03 RPM | 1 .96 RPM |
| SRP007412_liver | 0 .00 RPM | 1 .53 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1836 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1836 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_1836 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 11 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000020355 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000013114 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000019478 | 7 retrocopies |
retro_pabe_1836 , retro_pabe_2020, retro_pabe_2022, retro_pabe_2024, retro_pabe_2027, retro_pabe_2037, retro_pabe_3579,
|
| Rattus norvegicus | ENSRNOG00000016299 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000022002 | 1 retrocopy |