A. Motifs identified by maximum density
subgraph analysis
| SeqID or
accession or name |
Position | RIKEN Defintion/SPTR protein name | Motif
accession |
Result of HMMER searches |
| 7531
8146 Q9UFF7 Q9UH43 Q9V7X1 Q9VU34 |
372-411 552-591 206-245 847-886 827-866 |
unclassifiable
DNA segment, EST 573322 (MGI:1349561) Hypothetical 71.5 kDa protein (fragment)(Homo sapiens) DJ1014D13.3 (novel protein) (fragment) (Homo sapiens) CG15609 protein (Drosophila melanogaster) CG11259 protein (Drosophila melanogaster) |
MD00113 | EWFKLVLEKN
KLMRYESELL IMAQELELED HQSRLEQKLR
DWFKLIHEKH LLVRRESELI YVFKQQNLEQ RQADVEFELR QLLQLVDKKN SLVAEEAELM ITVQELNLEE KQWQLDQELR DWFKLIHEKH LLVRRESELI YVFKQQNLEQ RQADVEYELR QWFTLVNKKN ALLRRQMQLN ILEQEKDLER KYTMLNQELR QLFELVNEKN ELFRRQAELM YLRRQHRLEQ EQADIEHEIR |
| 8472
9875 12294 12790 14033 15271 22108 |
366-391 2-27 2-27 2-27 2-27 2-25 |
unclassifiable
transcript
Homeobox domain containing protein (InterPro IPR001356) unclassifiable dihydrolipoamide dehydrogenase (MGI:107450) unclassifiable transcript unclassifiable transcript unclassifiable |
MD00121 | WFLGFELRTF RRTVGVLTRR
AIYLSSP
WLLGFELLTF GRAVGCSYPL SH-LTSP WLLGFELLTF GRAVGCSYPL SH-LTTP WLLGFELWTF GRAVGCSYPL SH-LTSP WLLGFELRTF RRAVRCSYPL SH-LTSP WLLGFELRTF GRAVGCSYLL SH-LTSP WLLGFELRTF RRAVGALNHR AF---SP |
| 2213
7180 8388 8484 14092 19181 19684 |
3-22 117-136 16-35 3-22 17-36 52-71 |
related
to COSMID C49H3 (SPTR Q18720)*
unclassifiable transcript hypothetical protein receptor-like tyrosine kinase (MGI:101766) unclassifiable transcript unclassifiable transcript unclassifiable transcript |
MD00129 | FIPALKRWRQ
VDLCEFKASL
LIPALNRQRQ ADLCKFEDSQ LVPAPRRQRW AYLCEFKASL LIPALGRQRQ AVLCEFQTIL LVPVLGRHRQ ADPCEFKASL LIPALRRQRQ VDLCEFLANL LIPALRRQGQ AGLCEMKASL |
| 6649
14274 17278 23112 |
174-203
29-58 19-48 28-57 |
mutS homolog
3 (E. coli) (MGI:109519)
Protamine P1 containing protein (Pfam PF00260) Protamine P1 containing protein (Pfam PF00260) hypothetical protein |
MD00137 | HAFSRPARKN
AANRNLLWQK LYCLHLQEPE
YTRSRPARKN TANQNLLRQS FIAYIFRSKK HAFSRPARKN ATNRNLLRQK LYCLHLQEPE HTFTRPARKD ATNRNLLRQK LYCLHLQEPE |
| 17174
17937 21368 Q9WU72 |
7-35
46-74 32-56 137-163 |
unclassifiable
unclassifiable transcript unclassifiable transcript B-cell activating factor (Mus musculus) |
MD00139 | DVELSAPSPE
PCLPACHHVS RHDENGLNL
EVVLSATSPA PCLPACHHAS LPGNNGLNL DVELSAP-PT PCLPGC---Y LVDGNGLNL DVDLSAP-PA PCLPGCRH-S QHDDNGMNL |
| 7516
15434 18937 m_oatp1 m_oatp2-1 m_oatp2-c m_LST-1 r_oatp1 r_oatp2 r_oatp3 r_oatp5 r_OAT-K1 r_OAT-K2 r_LST-1 r_PGT h_OATP h_OATP8 h_OATP-B h_OATP-E h_OATP-F h_LST-1 h_PGT |
491-527
485-521 268-304 450-486 450-486 490-526 384-422 450-486 449-485 450-486 450-486 450-486 278-314 432-470 455-494 450-486 470-506 500-541 515-553 487-523 470-506 455-494 |
hypothetical
protein
hypothetical protein homolog to putative organic anion transporter organic anion transporting polypeptide 1 liver organic anion transporting polypeptide 2 cochlea organic anion transporter 2 liver specific transporter-1 organic anion transporting polypeptide 1 sodium-independent organic anion transporter 2 sodium-independent organic anion transporter 3 organic anion transporting polypeptide 5 sodium-independent organic anion transporter K1 sodium-independent organic anion transporter K2 liver-specific organic anion transporter prostaglandin transporter (PGT) sodium-independent organic anion transporter organic anion transporter 8 (OATP8) organic anion transporter OATP-B organic anion transporter OATP-E organic anion transporting polypeptide 14 liver-specific organic anion transporter prostaglandin transporter (PGT) |
MD00148 | YNPVCG-RDE
TQYFSPCFAG CKATKKLRKE K----TYYNC SC
YTSICG-RDE KEYFSPCFAG CKATKVSQTE K----TYYNC SC YSSVCG-RDE TEYFSPCFAG CLASKHLDYE K----TFYNC SC WDPVCG-DNG LAYMSACLAG CE-KSVGTGT N---MVFQNC SC WDPVCG-DNG LSYMSACLAG CE-KSVGTGT N---MVFQNC SC WEPMCG-DNG ITYVSACLAG CQ-SSSRSGK N---IIFSNC TC WEPVCG-ENG VTYISPCLAG CK-SFRGDKK LM-NIEFYDC SC WDPVCG-DNG VAYMSACLAG CK-KFVGTGT N---MVFQDC SC WDPVCG-DNG LAYMSACLAG CE-KSVGTGT N---MVFQNC SC WDPVCG-DNG LAYMSACLAG CK-KSVGTGT N---MVFQNC SC WDPVCG-DNG LAYITPCLAG CE-KSVGSGI N---MVLQDC SC WDPVCG-DNG LAYMSACLAG CE-KSVGTGT N---MVFHNC SC WDPVCG-DNG LAYMSACLAG CE-KSVGTGT N---MVFHNC SC WEPICG-ENG VTYISPCLAG CK-SFRGDKK PN-NTEFYDC SC FHPVCG-DNG VEYVSPCHAG CSSTNTSSEA SK-EPIYLNC SC WDPVCG-NNG LSYLSACLAG CE-TSIGTGI N---MVFQNC SC WEPVCG-NNG ITYLSPCLAG CK-SSSGIKK H---TVFYNC SC FNPVCDPSTR VEYITPCHAG CSSWVVQDAL DNSQVFYTNC SC YSPVCG-SDG LMYFSLCHAG CP-AATETNV DG-QKVYRDC SC WEPMCG-ENG ITYVSACLAG CQ-TSNRSGK N---IIFYNC TC WEPVCG-NNG ITYISPCLAG CK-SSSGNKK P---IVFYNC SC FHPVCG-DNG IEYLSPCHAG CSNINMSSAT SK-QLIYLNC SC |
| MD00113 is a leucine-zipper like motif. MD00148 represents a motif among the OATP family sequences. No SPTR hits were found for MD00121, MD00129 and MD00137. Accessions for the known OATP sequences are given after each OATP gene name (h:human, m:mouse, r:rat, m_oatp1: Genbank AB031813; m_oatp2-1: AB031814; m_oatp2-c: AY007379; m_LST-1: AB037202; r_oatp1: L19031; r_oatp2: U88036; r_oatp3: AF041105; r_oatp5: AF053317; r_OAT-K1: D79981; r_OAT-K2: AB012662; r_LST-1: r_PGT: SwissProt Q00910; h_OATP: U21943; h_OATP8: AJ251506; h_OATP-B: AB020687; h_OATP-E: AB031051; h_OATP-F: AF260704; h_LST-1: AF060500; h_PGT: U70867). SPTR entry Q18720 was available at the time of sequence analysis. In the meantime the entry has been deleted from SwissProt TrEMBL. |
B. UTR Functional Elements
| Functional Element |
|
Transcript |
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| 5'UTR or 3'UTR Located Elements | |||||
| Iron responsive element |
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| 5'UTR Located Elements | |||||
| Ribosomal mRNA TOP element |
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| 3'UTR Located Elements | |||||
| Histone 3'UTR stem-loop structure |
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| Seleno cysteine insertion sequence |
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| Erythroid 15-lipoxygenase differentiation control element |
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| AUUUA-containing class II AU rich element |
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| GLUT1 RNA stability determinant |
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| Vimentin 3'UTR element |
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| 1RIKEN clones
defined by significant similarity to known nucleotide sequences, protein
sequences or protein domains.
Number of annotated clones for each UTRsite pattern, classified on the basis of FANTOM's definitions: hypothetical protein, unclassifiable transcript, unclassifiable and all other categories (reported as "determined CDS"). Matching clones have been manually checked in order to compare the location of the pattern in the sequence to the location of the predicted CDS. The UTRsite functional pattern has been annotated only in clones where it was present in the correct position and fulfilling pattern specific features as described in the UTRsite database. |