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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattttcacttacttcgaggatattctttcttgcctacaacaatttgtgtagtttggaagcgaaacttaccttacaataacctggtttcataatctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGTCGGCCGCTTAAGGCTTCAAAACCATAGAAGAGAGCAAAAATGTTTTAGG

Basic information

species Oryza sativa
transcript LOC_Os01g37770.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g37770.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G015364_T02 (Zea mays), 3'ss of exon 10
gtaaattttcacttacttcgaggatattctttcttgcctacaacaatttgtgtagtttggaagcgaaacttaccttacaataacctggtttcataatctg-tacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGTCGGCCGCTTAAGGCTTCAAAACCATAGAAGAGAGCAAAAATGTTTTAGG
|||||         |||||  | | | ||||   ||  ||  |||||   |||| ||||  || | |||  | ||||||| ||| || |  | |||| || |||||| |||||||||||||||||||||||||| ||||| ||||| ||||| |||||  | ||||||  ||||    ||| ||||                    
gtaaa---------acttctggaaaactctt---tgtttatgacaatagatgtactttgctagtgcaaccaatcttacaa-aacttgctgccctaatttggtacagACGACGAAGAGGACATGCTTGAGCATTATTTAGCTGAACAATCAGGGAAGTCAACAGCTTAAC-CTTCTTGGCCAAAGAAA-------------------

upper sequence: LOC_Os01g37770.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G094595_T01 (Zea mays), 3'ss of exon 9
gtaaattttcacttacttcgaggatattctttcttgcctacaacaatttgtgtagtttggaagcgaaacttaccttacaataacctggtttcataatctg-tacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGTCGGCCGCTTAAGGCTTCAAAACCATAGAAGAGAGCAAAAATGTTTTAGG-
|||||     ||||| | || | | | ||||   ||  ||  ||| |   |||| ||||     | ||  || ||||||| ||| || |  | || | || |||||| || |||||||||||||||||||||||  ||||  |||| ||||  || || || ||||||  |||| |  ||| | ||   | |      |    ||  
gtaaa-----acttattccg-gaaaactctt---tgtttatgacattagatgtactttgtctatgtaagctatcttacaa-aacttgttcccctactttgatacagACGATGAAGAGGACATGCTTGAGCATTATCTAGCTCAACAATCAGAGAACTCAGCAGCTTAAC-CTTCTAGGCCAAACAAAGTACCTTTTCGGGCGCAGCT

upper sequence: LOC_Os01g37770.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G015364_T01 (Zea mays), 3'ss of exon 10
gtaaattttcacttacttcgaggatattctttcttgcctacaacaatttgtgtagtttggaagcgaaacttaccttacaataacctggtttcataatctg-tacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGTCGGCCGCTTAAGGCTTCAAAACCATAGAAGAGAGCAAAAATGTTTTAGG-
|||||         |||||  | | | ||||   ||  ||  |||||   |||| ||||  || | |||  | ||||||| ||| || |  | |||| || |||||| |||||||||||||||||||||||||| ||||| ||||| ||||| |||||  | ||||||  ||||    ||| ||||   | |      |    |   
gtaaa---------acttctggaaaactctt---tgtttatgacaatagatgtactttgctagtgcaaccaatcttacaa-aacttgctgccctaatttggtacagACGACGAAGAGGACATGCTTGAGCATTATTTAGCTGAACAATCAGGGAAGTCAACAGCTTAAC-CTTCTTGGCCAAAGAAAGTACCTTTTCAGGCACAACT

upper sequence: LOC_Os01g37770.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G094595_T02 (Zea mays), 3'ss of exon 10
gtaaattttcacttacttcgaggatattctttcttgcctacaacaatttgtgtagtttggaagcgaaacttaccttacaataacctggtttcataatctg-tacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGTCGGCCGCTTAAGGCTTCAAAACCATAGAAGAGAGCAAAAATGTTTTAGG
|||||     ||||| | || | | | ||||   ||  ||  ||| |   |||| ||||     | ||  || ||||||| ||| || |  | || | || |||||| || |||||||||||||||||||||||  ||||  |||| ||||  || || || ||||||  |||| |  ||| | ||                    
gtaaa-----acttattccg-gaaaactctt---tgtttatgacattagatgtactttgtctatgtaagctatcttacaa-aacttgttcccctactttgatacagACGATGAAGAGGACATGCTTGAGCATTATCTAGCTCAACAATCAGAGAACTCAGCAGCTTAAC-CTTCTAGGCCAAACAAA-------------------

upper sequence: LOC_Os01g37770.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G51730.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaaattttcacttacttcgaggatattctttcttgcctacaacaatttgtgtagtttggaagcgaaacttaccttacaataacctggtttcataatctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGTCGGCCGCTTAAGGCTTCAAAACCATAGAAGAGAGCAAAAATGTTTTAGG----
                      |   |||||| | |  ||||     || |  |  |  | | | ||   | |   | ||   | | ||||  |  |   ||||||||||||||| |||||||||||||| || || || ||  | || |     || ||  |   |     |||   |||  |    ||  | |   || ||      
--------------gtgaaatagtctttctttttggtttacacgcgattatcca--taagcaaccaatggttctcaagaaccgctttgttttttt-ttgatacagATGACGAAGAAGACATGCTTGAGCACTATTTGGCGGAGAAATCTGATTCTTCCGCTCCCCCAA----CAAGGACATGAAGCTAAGGGAGAGCCTTATATACTGA

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|55410164|gb|CV722540.1|CV722540
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|88353314|gb|CI654580.1|CI654580
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|29670377|gb|CB666652.1|CB666652
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|89186245|gb|CI262077.1|CI262077
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|88491923|gb|CI429195.1|CI429195
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|29670376|gb|CB666651.1|CB666651
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAAGACATGCTTGAGCATTAC
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTAC
EST: gi|88457374|gb|CI534372.1|CI534372
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|88958850|gb|CI381653.1|CI381653
EST:     CGAAGAGGAGGAAGAAGAGGAAAACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGTCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|86880817|gb|CI339152.1|CI339152
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|33665592|gb|CF296559.1|CF296559
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|86602635|gb|CI356999.1|CI356999
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|86885488|gb|CI318639.1|CI318639
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|86889359|gb|CI317159.1|CI317159
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|218496890|gb|FG962706.1|FG962706
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|88250975|gb|CI349205.1|CI349205
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|88255347|gb|CI354171.1|CI354171
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|88556147|gb|CI486457.1|CI486457
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
EST: gi|87010761|gb|CI312453.1|CI312453
EST:     CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG                         ATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT
genomic: CGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGT

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: 66 (upstream exon), 71 (downstream exon)
Score: 13

AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATGgtaaattttc ... atctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGTCGGCCGCTTAAGGCTTCAAAACCATAGAAGAGAGCAAAAATGTTTTAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagtttggaagcgaaacttaccttacaataacctggtttcataatctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGTCGGCCGCTTAAGGCTTCAAAACCATAGAAGAGAGCAAAAATGTTTTAGG
                           caataac  putative branch site (score: 13)
                        ttacaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattttcacttacttcgaggatattctttcttgcctacaacaatttgtgtagtttggaagcgaaacttaccttacaataacctggtttcataatctgtacagATGACGAAGAGGACATGCTTGAGCATTACTTAGCAGAACAGTCAGGCAAGTCGGCCGCTTAAGGCTTCAAAACCATAGAAGAGAGCAAAAATGTTTTAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA