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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgatgattttgtacagcatccttatcaaacttatacagaaaaggaacttgttaactatcgaaaaagaactgctttgttttggttatcctgattcagtctcttgtttctttacttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAGAGTTCTATGCCACCACCACCTTCATATGAAGAAATTAACGGTGTTTTCA

Basic information

species Oryza sativa
transcript LOC_Os10g36870.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g36870.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G002859_T03 (Zea mays), 3'ss of exon 6
gtactgatgattttgta-cagcatccttatcaaacttatacaga-----aaaggaacttgttaactatcgaaaaagaactgctttgttttggttatcctgattcag-tctcttgtttctttacttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAGAGTTCTATGCCACCACCACCTTCATATGAAGAAATTAACGGTGTTTTCA---
|| |||||| |||   | |  |||||||  ||  |||   ||       |||| || ||   |||| |||| ||| | ||| |  ||| || ||||| ||||| || | |||| ||| ||| ||     ||||||||||||||||||||||||| |||||||||||||   | |  ||||||||||| ||||| ||||| ||| ||||||||||| | || ||| | ||||   
gt-ctgatggtttcacatccacatcctttccatccttgcccattgtgctaaagaaagtttacaact-tcgagaaaaatctggtcggttatg-ttatcttgattgagctttcttattttttttct-----agATGGTATCTGAGCGCCAAAGAATCGAAGGAGCACCTC---CGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCATGA

upper sequence: LOC_Os10g36870.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G123624_T01 (Zea mays), 3'ss of exon 7
gtactgatgattttgtacagcatccttatcaa-acttatacagaaaaggaacttgttaactatcgaaaaagaactgctttgttttggttatcctgattcagtctcttgtttctttacttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAGAGTTCTATGCCACCACCACCTTCATATGAAGAAATTAACGGTGTTTTCA
||||||||| |||   |  ||||||||  ||   ||| | |   |||| ||||  |  |  ||||| |||   ||  |||||| || ||||||||||| |   |         ||| ||||  ||||||||||||||||||||||||||||||| ||||||||||| |  ||||||||||| ||||| ||||| ||| ||||||||||| | || ||| | ||||
gtactgatggtttatcattgcatcctttccagtgcttgtgc--caaagaaactc-tacatcatcgagaaaagtctagtttgttctg-ttatcctgattgaccattc-------ttatttttctagATGGTATCTGAGCGCCAAAGAATTGAAGGGGCACCTCCTCCGGTGGTTGAGAGTTCCATGCCTCCACCGCCTGCATATGAAGAAGTCAATGGTATATTCA
















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|699847|gb|D46138.1|D46138
EST:     GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
genomic: GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
EST: gi|163923564|gb|EG713305.1|EG713305
EST:     GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
genomic: GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
EST: gi|88224342|gb|CI224191.1|CI224191
EST:     GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
genomic: GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
EST: gi|89194036|gb|CI116473.1|CI116473
EST:     GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
genomic: GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
EST: gi|55828271|gb|AU069481.2|AU069481
EST:     GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAG                         ATGGTATCTGA-CGCCAAAGAATTGAAGGAGCACCTNCTTCA-CTGTTGAG
genomic: GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
EST: gi|86503263|gb|CI145896.1|CI145896
EST:     GAAG-TATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
genomic: GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
EST: gi|27546007|gb|CA764097.2|CA764097
EST:     GAAGTTATCACCAGAGGGTTCTGCAGATTCTCGATCAACTTGAAAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
genomic: GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
EST: gi|58686839|gb|CK075526.1|CK075526
EST:     AAGTTATCACCAGA-GGTTCTCGCAGATTCTTGATCAACTTGAAAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
genomic: AAGTTATCACCAGAGGGTTCT-GCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
EST: gi|86494493|gb|CI137126.1|CI137126
EST:     GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
genomic: GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
EST: gi|86504689|gb|CI147322.1|CI147322
EST:     GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
genomic: GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
EST: gi|88226552|gb|CI226468.1|CI226468
EST:     GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
genomic: GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
EST: gi|86493455|gb|CI136088.1|CI136088
EST:     GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
genomic: GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
EST: gi|87011472|gb|CI279381.1|CI279381
EST:     GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAG                         ATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG
genomic: GAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAG

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: 68 (upstream exon), 70 (downstream exon)
Score: 21

GTCGAATCTGAGAGAAGTTATCACCAGAGGGTTCTGCAGATTCTTGATCAACTTGAAAGAGAGgtactgatga ... acttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAGAGTTCTATGCCACCACCACCTTCATATGAAGAAATTAACGGTGTTTTCA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactgctttgttttggttatcctgattcagtctcttgtttctttacttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAGAGTTCTATGCCACCACCACCTTCATATGAAGAAATTAACGGTGTTTTCA
                    tcctgat  putative branch site (score: 21)
                               tctcttgtttctttac  putative PPT
                                      tttctttactttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgatgattttgtacagcatccttatcaaacttatacagaaaaggaacttgttaactatcgaaaaagaactgctttgttttggttatcctgattcagtctcttgtttctttacttttacagATGGTATCTGAGCGCCAAAGAATTGAAGGAGCACCTCCTCCAGCTGTTGAGAGTTCTATGCCACCACCACCTTCATATGAAGAAATTAACGGTGTTTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA