Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGAATTATGCTGATGCAAGCCACGTTTCTGCTGTCATTTTGGGTGGAGGCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagtgaaacactatttatatctaatgttgactactgtactgtgcagataatagatttttaattgtggataacatacttagaacttaagaaaaag...

Basic information

species Oryza sativa
transcript LOC_Os01g44220.6
intron # 3
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|1632029|gb|C19758.1|C19758
EST:     ACTTGGAGTTCAACTCTTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         T
genomic: ACT-GGAGTTCAACTCTTT-CCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttag-
EST: gi|1632029|gb|C19758.1|C19758
EST:     ACTTGGAGTTCAACTCTTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         T
genomic: ACT-GGAGTTCAACTCTTT-CCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttag-
EST: gi|1631746|gb|C19475.1|C19475
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTATTGACATCCCTATGGAGCAATTG
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTATTGACATCCCTATG-AGCAATTG
EST: gi|88586455|gb|CI704156.1|CI704156
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTATTG
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTATTG
EST: gi|88578726|gb|CI687673.1|CI687673
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTATTGACAT
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTATTGACAT
EST: gi|88310654|gb|CI672515.1|CI672515
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCT
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCT
EST: gi|88313641|gb|CI671770.1|CI671770
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGA
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGA
EST: gi|88313443|gb|CI671561.1|CI671561
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGT
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGT
EST: gi|88959416|gb|CI685897.1|CI685897
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGA
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGA
EST: gi|88379094|gb|CI681927.1|CI681927
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTATTGACATCC
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTATTGACATCC
EST: gi|88310738|gb|CI672605.1|CI672605
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTA
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTA
EST: gi|88578267|gb|CI687187.1|CI687187
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGAT
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGAT
EST: gi|88369721|gb|CI680389.1|CI680389
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTA
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTA
EST: gi|88321573|gb|CI672705.1|CI672705
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGA
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGA
EST: gi|88851762|gb|CI674964.1|CI674964
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTATTGACATCCCTATGAGCAATTGC
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTATTGACATCCCTATGAGCAATTGC
EST: gi|88378739|gb|CI681555.1|CI681555
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTATTGACATC
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTATTGACATC
EST: gi|88576805|gb|CI673331.1|CI673331
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAG
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAG
EST: gi|88369747|gb|CI680418.1|CI680418
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAG
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAG
EST: gi|88321531|gb|CI672660.1|CI672660
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTATTGA
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTATTGA
EST: gi|88451782|gb|CI694552.1|CI694552
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGAT
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGAT
EST: gi|88414466|gb|CI691632.1|CI691632
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTATTGACATCCCTATGAGCAATTGC
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTATTGACATCCCTATGAGCAATTGC
EST: gi|88371876|gb|CI681387.1|CI681387
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTA
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTA
EST: gi|88461692|gb|CI695535.1|CI695535
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCT
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCT
EST: gi|88331522|gb|CI675859.1|CI675859
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCT
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCT
EST: gi|88463678|gb|CI696154.1|CI696154
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTAT
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTAT
EST: gi|66922783|gb|CX109631.1|CX109631
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTATTGACATCCCTATGAGCAATTGC
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTATTGACATCCCTATGAGCAATTGC
EST: gi|88582923|gb|CI699388.1|CI699388
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTATTGACATC
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTATTGACATC
EST: gi|88361961|gb|CI682139.1|CI682139
EST:     GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCT                         GTTCCTGTTGGAGGATGTTACAGGCTTATTGACATCCCTATGAGC
genomic: GCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTATTGACATCCCTATGAGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 75 (downstream exon)
Score: 454

AAAGAATTATGCTGATGCAAGCCACGTTTCTGCTGTCATTTTGGGTGGAGGCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagt ... tattacttagGTTCCTGTTGGAGGATGTTACAGGCTTATTGACATCCCTATGAGCAATTGCTTCAATAGCGGAATAAATAAAATATTTGTGATGACTCAGTTCAATTCTG




<











<


<









Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGAATTATGCTGATGCAAGCCACGTTTCTGCTGTCATTTTGGGTGGAGGCACTGGAGTTCAACTCTTTCCTCTGACAAGCACAAGGGCTACCCCCGCTgtaagaaagtgaaacactatttatatctaatgttgactactgtactgtgcagataatagatttttaattgtggataacatacttagaacttaagaaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa