FNIP repeats
These sequences are coding for FNIP repeats (Source: Pandit - PF05725). Magnolia classifies them as protein coding sequences and predicts the correct reading frame for each sequence.
Magnolia multiple alignment of nucleic sequencesQ8T126_DICDI/754-797 TTTAATCAACCTTTAAAACTTGGT---GTAATTCCTGATTCTTGTACTTTTATTCAATTT Q8SSW4_DICDI/189-234 TTCAATCAATCTTTAAAAGGTAAT---TGGCTATCATCAAATATTAAATCATTGAAATTT Q8T126_DICDI/514-556 CATTCGAAATCTTTAAAACCAAGA---GATATACCAAAGAGTATCATTCATTTACAATTA Q8MP78_DICDI/367-412 TTTAATCAACCATTTGATCAAGATAATATATTACCATCAACATTAACTCATTTAATATTA Q8T126_DICDI/754-797 GGTTCACAATTTAAT---CAATCATTAGAACCAATG------GTTATACCATCATCAGTT Q8SSW4_DICDI/189-234 GGTAATGAATTCAGT---CAACCAATTAGTGACATTAATAATTTTTTACCAAAATCATTA Q8T126_DICDI/514-556 CCA---AATTATAAT---TTAAAAATTCGTAGAAATTCA------ATACCTGATCAAACA Q8MP78_DICDI/367-412 AATAATAATTATTCAATTGAAAATTTATTAAAAATTAAA------TTACCAATTTCATTA Q8T126_DICDI/754-797 AAAGAATTAATATTTGGTTCACAA Q8SSW4_DICDI/189-234 ACATCATTAAATTTACCATCAAAA Q8T126_DICDI/514-556 AAATTCTTAATATTAGGTTCTGAT Q8MP78_DICDI/367-412 ACATTTTTATCACTATCAAAAAATMagnolia multiple alignment for predicted amino-acid sequences
Q8T126_DICDI/754-797 FNQPLKLG-VIPDSCTFIQFGSQFN-QSLEPM--VIPSSVKELIFGSQ Q8SSW4_DICDI/189-234 FNQSLKGN-WLSSNIKSLKFGNEFS-QPISDINNFLPKSLTSLNLPSK Q8T126_DICDI/514-556 HSKSLKPR-DIPKSIIHLQLP-NYN-LKIRRNS--IPDQTKFLILGSD Q8MP78_DICDI/367-412 FNQPFDQDNILPSTLTHLILNNNYSIENLLKIK--LPISLTFLSLSKNReference hand-curated multiple alignment (Pandit)
Q8T126_DICDI/754-797 FNQP-LKLGVIPDSCTFIQF-GSQFN-QSLE--PMVIPSSVKELIFGSQ Q8SSW4_DICDI/189-234 FNQS-LKGNWLSSNIKSLKF-GNEFS-QPISDINNFLPKSLTSLNLPSK Q8T126_DICDI/514-556 HSKS-LKPRDIPKSIIHLQL--PNYN-LKIR--RNSIPDQTKFLILGSD Q8MP78_DICDI/367-412 FNQPFDQDNILPSTLTHLIL-NNNYSiENLL--KIKLPISLTFLSLSKNClustalW alignment of nucleic sequences
Q8T126_DICDI/754-797 --TTTAATCAACCTTTAAAACTTGGTGTAATTCCTGATTCTTGTACTTTTATTCA----- Q8SSW4_DICDI/189-234 --TTCAATCAATC-TTTAA----AAGGTAATTGGCTATCATCAAATATTAAATCATTGAA Q8T126_DICDI/514-556 CATTCGA--AATCTTTAAAACC-AAGAGATATACCAAAGAGTAT-CATTCATTTAC---- Q8MP78_DICDI/367-412 --TTTAATCAACCATTTGATC--AAGATAATATATTACCATCAA-CATTAACTCATTTAA Q8T126_DICDI/754-797 -ATTTGGTTCACA----ATTTAATCAATCATTAGAACCAATGGTTAT---ACCATCATCA Q8SSW4_DICDI/189-234 -ATTTGGTAATGAATTCAGTCAACCAATTAGTGACATTAATAATTTT-TTACCAAAATCA Q8T126_DICDI/514-556 -AATTACCAAATT-----ATAATTTAAAAATT--CGTAGAAATTCAA--TACCTGATCAA Q8MP78_DICDI/367-412 TATTAAATAATAA--TTATTCAATTGAAAATT--TATTAAAAATTAAATTACCAATTTCA Q8T126_DICDI/754-797 GTTAAAGAATTAATATTTGGTTCACAA--- Q8SSW4_DICDI/189-234 TTAACATCATTAAATTTACCATCAAAA--- Q8T126_DICDI/514-556 ACAAAATTCTTAATATTAGGTTCTGAT--- Q8MP78_DICDI/367-412 TTAACATTTTTA---TCACTATCAAAAAAT
Transfer RNAs
This data set contains five tRNA sequences. It comes from Bralibase II, tRNA 13. Magnolia classifies these sequences as non-coding RNA genes, and provides a multiple alignment that is very similar to the hand-curated structural alignment. In contrast, ClustalW produces a mutliple alignment which is not compatible with the secondary structure, especially regarding the first sequence (X61674).
Reference structural alignment
X61674.1-10 GGAGAGATGGCTGAGT-GGACTAAAGCGGCGGATTGCTAATCCGTT-GTACAATT Y00430.1-24 GGGGGTGTAGCTCAGT-GGT--AGAGCGCATGCTTTGCATGTATGAG-------- X12977.1-94 GCGCCCGTAGCTCAGCTGGAT-AGAGCGCTGCCCTCCGGAGGCAGAG-------- X54300.1-29 GGGTTATTAGCTCAGTTGGTT-AGAGCACACCCCTGATAAGGGTGAG-------- AJ271079.2- TCCTCAGTAGCTCAGT-GGT--AGAGCGGTCGGCTGTTAACCGATTG-------- X61674.1-10 TTTTTGTAC--CGAGGGTTCGAATCCCTCTCTTTCCG Y00430.1-24 ---------GTCTTGGGTTCAATCCCCAGCATCTCCA X12977.1-94 ---------GTCACAGGTTCGAATCCTGTCGGGCGCA X54300.1-29 ---------GTCCCTGGTTCAAATCCAGGATAACCCA AJ271079.2- ---------GTCGTAGGTTCGAATCCTACTTGGGGAG
Magnolia alignment
X61674.1-10 --GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCGTTGTACAATT Y00430.1-24 GGGGG-TG-TAGCTCAG-TGG-TAGAGCGCATGCTTTGCATGTATGAGG----T- X12977.1-94 GCGCC-CG-TAGCTCAGCTGGATAGAGCGCTGCCCTCCGGAGGCAGAGG----T- X54300.1-29 GGGTT-AT-TAGCTCAGTTGGTTAGAGCACACCCCTGATAAGGGTGAGG----T- AJ271079.2- TCCTC-AG-TAGCTCAG-TGG-TAGAGCGGTCGGCTGTTAACCGATTGG----T- ((((( (((((( )))))) X61674.1-10 TTTTTGTACCGAGGGTTCGAATCCCTC---TCTTTCCG Y00430.1-24 --------C-TTGGGTTC-AATCCCCAGCATCT--CCA X12977.1-94 --------C-ACAGGTTCGAATCCTG-TCGGGC--GCA X54300.1-29 --------C-CCTGGTTCAAATCCAGG-ATAAC--CCA AJ271079.2- --------C-GTAGGTTCGAATCCTAC-TTGGG--GAG ((((( ))))) ))) ))
ClustalW alignment
X61674.1-10 GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCGTTGTACAATTTT Y00430.1-24 GGGGGTGTAGCTCAGT--GGTAGAGCGCATGCTTTGCATGTATGAGGTCTTGGGT X12977.1-94 GCGCCCGTAGCTCAGCTGGATAGAGCGCTGCCCTCCGGAGGCAGAGGTCACAGGT X54300.1-29 GGGTTATTAGCTCAGTTGGTTAGAGCACACCCCTGATAAGGGTGAGGTCCCTGGT AJ271079.2- TCCTCAGTAGCTCAGT--GGTAGAGCGGTCGGCTGTTAACCGATTGGTCGTAGGT X61674.1-10 TTTGTACCGAGGGTTCGAATCCCTCTCTTTCCG Y00430.1-24 TCAATCCCCAGCATCTCCA-------------- X12977.1-94 TCGAATCCTGTCGGGCGCA-------------- X54300.1-29 TCAAATCCAGGATAACCCA-------------- AJ271079.2- TCGAATCCTACTTGGGGAG--------------