Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggatccgttcttgcttgaagaattttcttgttgcctggtgtggtttcttgatctgttgcagatttgtgatgtgtttggtggtggattgttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG

Basic information

species Oryza sativa
transcript LOC_Os08g33920.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G152552_T02 (Zea mays), 3'ss of exon 1
gtacgg---atccgttcttgcttgaagaattttcttgttgcctggtgtggtttcttgatctgttgcagatttgtgat-gtgtttggtggtggattg--ttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG--------------------
|| ||     || |||| | | ||    || |    |  | |   | ||||||||| ||||||      ||  || | || ||   ||||    ||  || ||||||| |||| |||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||| |||||||||                    
gttcgccccgtctgttcattcctgctcgatatgggaggggtc---tttggtttctttatctgtgttgtgttcttggttgtattaattggttcgctggattcttgcagGCGGGAAGCTTGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGTGCCCCGTCACCGGGAAGAAAATCCAGGGGGTGAGTGATTGATTGTTAGC

upper sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G152552_T01 (Zea mays), 3'ss of exon 1
gtacgg---atccgttcttgcttgaagaattttcttgttgcctggtgtggtttcttgatctgttgcagatttgtgat-gtgtttggtggtggattg--ttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
|| ||     || |||| | | ||    || |    |  | |   | ||||||||| ||||||      ||  || | || ||   ||||    ||  || ||||||| |||| |||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||| |||||||||
gttcgccccgtctgttcattcctgctcgatatgggaggggtc---tttggtttctttatctgtgttgtgttcttggttgtattaattggttcgctggattcttgcagGCGGGAAGCTTGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGTGCCCCGTCACCGGGAAGAAAATCCAGGGG

upper sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G820996_T03 (Zea mays), 3'ss of exon 1
gtacggatccgttcttgcttgaagaattttcttgtt----gcctggtgtggtttcttgatctgttgcagatttgtgatgtgtttggtgg-tggattg--ttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG--------------------
       | ||  |   || |  |    | || | |    ||   || ||||||||||||||||  |    |  || |    ||| ||| |    ||  || |||||||||||| |||||||||||| ||||| ||||||||||||||||| || |||||||||||||||||||||||||||||||||                    
------gttcgccccatctggtcgttcctgctcgatctgggcgcagtctggtttcttgatctgtatcgcgctcttggttgtattgatggcttcgctggatttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGGTGAGTGATTACTTGTTAGG

upper sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G820996_T01 (Zea mays), 3'ss of exon 1
gtacggatccgttcttgcttgaagaattttcttgttgcctggtgtggtttcttgatctgttgcagatttgtgatgtgtttggtgg-tggattg--ttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
         ||||| |||| ||       ||| |  ||   || ||||||||||||||||  |    |  || |    ||| ||| |    ||  || |||||||||||| |||||||||||| ||||| ||||||||||||||||| || |||||||||||||||||||||||||||||||||
-------gtcgttcctgctcga-------tctgg--gcgcagtctggtttcttgatctgtatcgcgctcttggttgtattgatggcttcgctggatttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG

upper sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G820996_T02 (Zea mays), 3'ss of exon 1
gtacggatccgttcttgcttgaagaattttcttgtt----gcctggtgtggtttcttgatctgttgcagatttgtgatgtgtttggtgg-tggattg--ttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
       | ||  |   || |  |    | || | |    ||   || ||||||||||||||||  |    |  || |    ||| ||| |    ||  || |||||||||||| |||||||||||| ||||| ||||||||||||||||| || |||||||||||||||||||||||||||||||||
------gttcgccccatctggtcgttcctgctcgatctgggcgcagtctggtttcttgatctgtatcgcgctcttggttgtattgatggcttcgctggatttttgcagGTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG

upper sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA18G14980.1 (Glycine max), 3'ss of exon 1
-------gtacggatccgttcttgcttgaagaattttcttgttgcctggtgtggtttcttgatc-----tgttgcagatttgtgatgtgtttggtggtggattgttgttg----cagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
       ||       || |     | |  |  | ||||   | | ||| |||   | |    |     ||||  | |  |    |||  |  | ||||| | |||||||    ||||||| | |||||| || |||  ||||||||||||||| ||||| || |||||||| ||||| || |||| ||| || |||
gtaaactgtcttcgctcgcttcgcatcgtcgtttattctcact-catggcgtgtcgtttgcgccgcgagtgttctaaaaatagactgtaatgtgcggtggctggttgttgaatgcagGTGGCAAGCTTGTTTATCAGACCACGAAGAAGAGGGCCAGCGGACCCAAGTGCCCTGTCACTGGAAAGAGGATTCAAGGG

upper sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G41280.1 (Glycine max), 3'ss of exon 1
------------------------gtacggatccgttcttgcttgaagaattttc-ttgttgcctggtgtggtttcttgatctgttgcagatttgtgatg-tgtttggtggtggattgttgt-tgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
                          ||     ||||  | ||     |     | |||| |  | | |  |   |  |  ||     | || | |  |  |||  ||| |  ||||||||  ||||||||| | |||||| || |||  ||||||||||||||| ||||| || |||||||| ||||| || |||| ||| || |||
gtaaataaactctcttcgctcgcctcacatcgtcgtttattctcactcacggcgcgttgtcgttttgcgccgccgcgagggct-ccaaaaatatattttaatgtgcggttgctgattgttgaatgcagGTGGCAAGCTTGTTTATCAGACCACGAAGAAGAGGGCCAGCGGACCCAAGTGCCCTGTCACTGGAAAGAGGATTCAAGGG

upper sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA01G05740.1 (Glycine max), 3'ss of exon 1
----------------------------------gtacggatccgttcttgcttgaagaattttcttgttgcctggtgtggtttcttgatctgttgcagatttgtgatgt-------gtttggtggtggattgttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
                                  |  |||| |  || ||| ||      || | |||||            || ||| | |      | | ||    ||       |||||||  ||      |  ||||||||||| ||| || || |||   || ||||||||||| ||||| || |||||||||||||| || |||| ||| ||||||
gtaatcaaatccctccctcactgattatgcttcggatcggaacaatttttgtttttgtttttgttttgttttaaaaaaaaagtttttggtattaattggttctgctgggtacgtcttgtttggttctgtgggaataatgcagGTGGGAAGCTCGTTTATCAGACTACCAAGAAGAGGGCCAGCGGACCCAAGTGCCCCGTCACTGGCAAGAGGATTCAGGGG

upper sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G11920.1 (Glycine max), 3'ss of exon 1
-----------------------------------gtacggatccgttcttgcttgaagaattttcttgttgcctggtgtggtttcttgatctgttgcag-atttgtgatgtgtttggtggtggattgttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
                                    | ||  |  | |     | | |  | ||| ||| |   |  | | |  | || ||  |||        | || ||||||||||| ||      |  ||||||||||| ||| || || |||  ||| ||||||||||| |||||||| |||||||||||||| || |||| ||| ||||||
gtaatcaaatccctcttcggaacccctcactcactcttcgattatgcttcgaatcggaacaattt-ttgctttttaattttgggtattaattggttctgacgggtatgttgtgtttggtgatgtgggaataatgcagGTGGGAAGCTCGTTTATCAGACCACCAAGAAGAGGGCCAGCGGGCCCAAGTGCCCCGTCACTGGCAAGAGGATTCAGGGG

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|163928141|gb|EG713573.1|EG713573
EST:     TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAG                         GTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
genomic: TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
EST: gi|88981573|gb|CI027190.1|CI027190
EST:     ACCAGGGTCGTCAAGACCCCAG                         GTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
genomic: ACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
EST: gi|8956388|gb|BE230175.1|BE230175
EST:     TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAG                         GTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
genomic: TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
EST: gi|7273822|gb|AU083366.1|AU083366
EST:     TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAG                         GTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
genomic: TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
EST: gi|88237405|gb|CI237254.1|CI237254
EST:     AAGTCGAACCAGACCAGGGTCGTCAAGACCCCAG                         GTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
genomic: AAGTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
EST: gi|86831154|gb|CI295631.1|CI295631
EST:     TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGATCCCAG                         GTGGGAGGCTTGTGTACCAGTACAC
genomic: TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACAC
EST: gi|58669464|gb|CK058150.1|CK058150
EST:     TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAG                         GTGGGAGGCTTGTGTATCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
genomic: TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
EST: gi|55410863|gb|CV723239.1|CV723239
EST:     TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAG                         GTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
genomic: TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
EST: gi|88982496|gb|CI027965.1|CI027965
EST:     TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGATCCCAG                         GTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
genomic: TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
EST: gi|56158237|gb|C91722.2|C91722
EST:     TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAG                         GTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
genomic: TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
EST: gi|88719483|gb|CI742993.1|CI742993
EST:     TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAG                         GTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
genomic: TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
EST: gi|88309305|gb|CI655313.1|CI655313
EST:     TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAG                         GTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
genomic: TCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT
EST: gi|15849588|gb|BI797850.1|BI797850
EST:     GTCGAACCAGACCAGGTTCTTCAAGACCCCAG                         TTGGGAGGCTTGTGTATCAGTACACGAAGAAGA-GGCGA-C-GGCCGAAGT
genomic: GTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGT

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), 72 (downstream exon)
Score: 158

CGCGGCGGCGGCGGTGGCGAGATGGTGCAGCGGCTCACCTACCGGAAGCGTCACAGCTACGCGACTAAGTCGAACCAGACCAGGGTCGTCAAGACCCCAGgtacggatcc ... gttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcttgatctgttgcagatttgtgatgtgtttggtggtggattgttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG
   tcttgat  putative branch site (score: 158)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggatccgttcttgcttgaagaattttcttgttgcctggtgtggtttcttgatctgttgcagatttgtgatgtgtttggtggtggattgttgttgcagGTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG