RetrogeneDB ID: | retro_pabe_3579 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | Un:23404451..23405908(-) | ||
| 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_3579
ATGGGGCAGCCACCTGGCGAGTCTGACATGGCTGTCAGCGACGCGCTGCTCCCATCTTTCTCCACGTTCGCGTCTGGCCC
GGCGGGAAGGGAGAAGACACTGCGTCAAGCAGGTGCCCCGAATAACCGCTGGCGGGAGGAGCTCTCCCACATGGAGCGAC
TTCCCCCGGTGCTTCCCGGCCGCCCCTATGACCTGGCGGCGGCGACCGTGGCCACAGACCTGGAGAGCGGCGGAGCCGGT
GCGGCTTGCGGCGGTAGCAACCTGGCGCCCCTACCTCGGAGAGAGACCGAGGAGTTCAGCGATCTCCTGGACCTAGACTT
TCATCCTCTCCAATTCGCTGACCCATCCTCCGGAGTCAGTGGCCGCCACCGTGTCCTCGTCAGCGTCAGCCTCCTCCTCC
TCCTCGTCGTCCCCGTCGAGCAGCGGCCCTGCCAGCGCGCCCCCCACCTGCAGCTTCACCGATCCCATCCGGGCCGGGAA
ACACCCGGGCGTGGCGCCGGGCGGCACGGGCGGAGGCCTCTTGATGGCAGGGAGTCCGCTCCCCCTCCGACGGCTCCCTT
CAACCTGGCGGACATCAACGACGTGAGCCCCTCGGGCGGCTTCGTGGCCGAGCTCCTGCGGCCAGAATTGGACCCGGTGT
ACATTCCGCCGCAGCAGCCGCAGCCGGCAGGTGCCGGGCTGATGGGCAAGTTCGTGCTGAAGGCGTCGCTGAGCGCCCCT
GGCAGCGAGTAGGGCAGCCTGTCGGTCATCAGCGTCAGCAAAGGCAGCCCTGACGGCAGCCACCCGGTGGTGGTGGCGCC
CTACAACGGCGGGCCGCCGCGCACGTGTCCCAAGATCAAGCGGGAGGCGGTCTCCTGGTGCTCCCACTTGGGCGTTGGAA
CCCCTCTCAGCAATGGCCACCGGCCGGCTGCACACGACTTCCCCCTGGGGCGGCAGCTCCCCAGCAGGACTACCCCGACC
CTGGGTCTGGAGGAAGTGCTGAGCAGCCGGGACTGTCACCCTGCCCTGCCGCTTCCCCGCCCTCTACCCCCCTCCGGCTT
CCATCCCCACCCGGGGCCCAAGTACCCATCCTTCCTGCCCGACCAGATGCAGCCGCAAGTCCCGTCGCTCCATTACCAAG
AGCTCATGCCACCCGGTTCCTGCATGCCGGAGGAGCCCAAGCCAAAGAGGGGAAGACGATCGTGGCCCCGAAAAGGGCCG
CCACCCACACTTGTGATTACGCGGGCTGCGGCCAAGCCTACACAAAGAGTTCCCATCTCAAGGCACACCTGCGAACCCAC
ACAGGTGAGAAACCTTACCACTGTGACTGGGACGGCTGTGGATGGAAATTCGCCCGCTCGGATGAACTGACCAGGCACTA
CCGTAAACACACTGGGCACTGCCCATTCCAGTGCCAAAAATGCGACCGAGCATTTTCCAGGTCGGACCACCTCGCCTTAC
ACATGAAGAGGCATTTT
ORF - retro_pabe_3579 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.23 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MRQPPGESDMAVSDALLPSFSTFASGPAGREKTLRQAGAPNNRWREELSHMKRLPPVLPGRPYDLAAATV |
| M.QPPGESDMAVSDALLPSFSTFASGPAGREKTLRQAGAPNNRWREELSHM.RLPPVLPGRPYDLAAATV | |
| Retrocopy | MGQPPGESDMAVSDALLPSFSTFASGPAGREKTLRQAGAPNNRWREELSHMERLPPVLPGRPYDLAAATV |
| Parental | ATDLESGGAGAACGGSNLVPLPRRETEEFNDLLDLDF-ILSNSLTHPPESVAATVSSSASASSSSS--PS |
| ATDLESGGAGAACGGSNL.PLPRRETEEF.DLLDLDF.ILSNSLTHPPESVAATVSSSASASSSSS..PS | |
| Retrocopy | ATDLESGGAGAACGGSNLAPLPRRETEEFSDLLDLDF>ILSNSLTHPPESVAATVSSSASASSSSSSSPS |
| Parental | SSGPASAPSTCSFTYPIRAGNDPGVAPGGTGGGLLY-GRESAPPPTAPFNLADINDVSPSGGFVAELLRP |
| SSGPASAP.TCSFT.PIRAG..PGVAPGGTGGGLL..GRESAPPPTAPFNLADINDVSPSGGFVAELLRP | |
| Retrocopy | SSGPASAPPTCSFTDPIRAGKHPGVAPGGTGGGLLM<GRESAPPPTAPFNLADINDVSPSGGFVAELLRP |
| Parental | ELDPVYIPPQQPQPPGGGLMGKFVLKASLSAPGSEYGSPSVISVSKGSPDGSHPVVVAPYNGGPPRTCPK |
| ELDPVYIPPQQPQP.G.GLMGKFVLKASLSAPGSE.GS.SVISVSKGSPDGSHPVVVAPYNGGPPRTCPK | |
| Retrocopy | ELDPVYIPPQQPQPAGAGLMGKFVLKASLSAPGSE*GSLSVISVSKGSPDGSHPVVVAPYNGGPPRTCPK |
| Parental | IKQEAVSSCTHLGAGPPLSNGHRPAAHDFPLGRQLPSRTTPTLGLEEVLSSRDCHPALPLPPGFHP---H |
| IK.EAVS.C.HLG.G.PLSNGHRPAAHDFPLGRQLPSRTTPTLGLEEVLSSRDCHPALPLP....P...H | |
| Retrocopy | IKREAVSWCSHLGVGTPLSNGHRPAAHDFPLGRQLPSRTTPTLGLEEVLSSRDCHPALPLPRPLPPSGFH |
| Parental | P--GPNYPSFLPDQMQPQVPPLHYQELMPPGSCMPEEPKPKRGRRSWPR-KRTATHTCDYAGCGKTYTKS |
| P..GP.YPSFLPDQMQPQVP.LHYQELMPPGSCMPEEPKPKRGRRSWPR.KR.ATHTCDYAGCG..YTKS | |
| Retrocopy | PHPGPKYPSFLPDQMQPQVPSLHYQELMPPGSCMPEEPKPKRGRRSWPR<KRAATHTCDYAGCGQAYTKS |
| Parental | SHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYRKHTGHRPFQCQKCDRAFSRSDHLALHMKRHF |
| SHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYRKHTGH.PFQCQKCDRAFSRSDHLALHMKRHF | |
| Retrocopy | SHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYRKHTGHCPFQCQKCDRAFSRSDHLALHMKRHF |
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 .00 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_3579 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3579 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3579 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 |