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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacatatgctcccctttcagatgtttattgatacttctgctcttatatggatactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA

Basic information

species Oryza sativa
transcript LOC_Os01g63890.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G099007_T01 (Zea mays), 3'ss of exon 1
gtatg-acatatgctcccctttcagatgtttattgatac---ttctgctcttatatgga----tactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA
||||| ||| ||| |           |   || ||||     || |   ||   |  |     ||||||  | ||   |||||| ||||||||||||  |||||||||| ||||||||||| ||||| |||||||| |||||||||||||| |||||||| || |||||||||||||||||||| ||
gtatgcacagatggttattgagacactcactactgatgtcagttgtttcctggcacaggattgtactaacgttatgccctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCGCTCTGGCCTATTTTCCGTATTTCTCATCAAAGGAGCCGCTACATATATGATCTTTACTA

upper sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G018464_T01 (Zea mays), 3'ss of exon 6
gtatgacatatgctcccctttcagatgtttattgatacttctgctcttatatggatactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA
                          ||   |   || |||    |  |      || |||   |||   |||||| ||||||||||||  |||||||||||||||||||||| ||||| |||||||| ||| || ||||||| |||||||| || | || |||||||| |||||| ||
--------------------------gtaagtctttatttcctagcacaagattgtaataacgccatgctctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTATCTGTATTTCTCATCAAAGGAGCCACTTCATATATGGTCTTTACTA

upper sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G095670_T02 (Zea mays), 3'ss of exon 2
-------------gtatgacat--atgctcccctttcagatgtttattgatacttctgctcttatatgga----tactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA
              ||| |  |  | || | |    | |||||   ||| || || |   ||   |  |     ||||||    ||   |||||| ||||||||||||  |||||||||||||||||||||| ||||| |||||||| |||||||| ||||| |||||||| || ||||||||||| |||||||| ||
gtaggcacatacgctattaatttgaggcactcgccactgatgtcagttgttatttatttcctagcacaggatcgtactaacgctatgccctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGCATTTCTCATCAAAGGAGCCGCTACATATACGATCTTTACTA

upper sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G174792_T01 (Zea mays), 3'ss of exon 8
gtatgacatatgctcccctttcagatgtttattgatacttctgctcttatatggatactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA
                          ||   | | || |||    |  |      || |||   |||   ||| || ||||||||||||  |||||||||||||||||||||| ||||| |||||||| |||||||||||||| |||||||| || | || ||||||||||||||| ||
--------------------------gtaagtcgttatttcctagcacaggattgtaataacgccatgctctcgtgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGTATTTCTCATCAAAGGAGCCACTTCATATATGATCTTTACTA

upper sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G129979_T01 (Zea mays), 3'ss of exon 2
gtatgacatatgctcccctttcagatgtttattgatacttctgctcttatatggatactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA
                          ||   | | || ||||   |  |      || |||  ||||   |||||| ||||||||||||  |||||||||||||||||||||| ||||| |||||||| |||||| ||||||| |||||||| || | || |||||||| |||||| ||
--------------------------gtaagtcgttatttcttagcacaggattgtaataacgtcatgctctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCTGTATTTCTCATCAAAGGAGCCACTTCATATATGGTCTTTACTA

upper sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 2
----------------gtatgacatatgctcccctttcagatgtttattgatacttctgctctta-tatgga----tactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA
                 |       | ||   |  | | |||||   ||| || ||    || ||  |  |     ||||||    ||   |||||| ||||||||||||  |||||||||| ||||||||||| ||||| |||||||| |||||||| ||||| |||||||| || ||||||||||| |||||||||||
gtaggcacatacggctattcatttgaggcattcactactgatgtcagttgttattttatttcctagcacaggatcgtactaacgctatgccctcatgcagCTGAAAATGATCCACATGATGGAAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGCATTTCTCATCAAAGGAGCCGCTACATATACGATCTTTATTA

upper sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G070451_T01 (Zea mays), 3'ss of exon 1
----------------gtatgacatatgctcccctttcagatgtttattgatacttctgctcttatatgga----tactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA
                 |       | || | |  | | ||||||  ||| || || | | ||   |  |     |||||||   ||   || ||| ||||||||||||  |||||||||||||||||||||| ||||| |||||||| |||||||| ||||| |||||||| || ||||||||||||||| |||| ||
gtaggcacagatggctattcatttgaggcactcgctactgatgttagttgttatttattccctagcacaggatcgtactaatgctatgcccttatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGCATTTCTCATCAAAGGAGCCGCTACATATATGATGTTTACTA

upper sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 2
-----------gtatgacatatgctcccctttcagatgtttattgatacttctgctcttatatggatactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA
              | |   | || | |  | | |||||   ||| |  | |||       || | ||||||  | ||   |||||| ||||||||||||  |||||||||||||||||||||| ||||| |||||||| |||||||||||||| |||||||| || |||||||||||||||||||| ||
gtatgcacaaacggttattgaggcactcactactgatgtcagttgtt--tcctggcacaggattg-tactaacgttatgccctcatgcagCTGAAAATGATCCACATGATGGGAAGAGAAAGTGTGAAGCTCTCTGGCCTATTTTCCGTATTTCTCATCAAAGGAGCCGCTACATATATGATCTTTACTA

upper sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 2
---------------------gtatgacat---atgctcccctt-tcagatgtttattgatacttctgctcttatatggatactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA
                      ||   |     ||| |  | || ||   |||||  |||   |      || | |  || ||   | |       |     ||||||||||||| |||||||||| |||||||| || || || || ||||| ||||||   ||  | ||||| |  || || || || | |||||||||  |
gttattctctttttctcatgcatacagctctgaatgttgtctttgtcgcttgtttgctgaacttataaaactaacaatgacaccgttctatgtcttttgaacagCTGAAAATGACCCACATGATGGTAAGAGAAAATGTGAGGCACTATGGCCGATTTTCAAAATAGCACATCAGAAGAGCCGTTATATTTTTGATCTTTACCA

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|88436678|gb|CI691412.1|CI691412
EST:     GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAG                         CTGAAAATGACCCACCATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCC
genomic: GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACAC-ATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCC
EST: gi|89187948|gb|CI009932.1|CI009932
EST:     CCAAAATGAGGGAAG                         CTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
genomic: CCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
EST: gi|88309294|gb|CI655302.1|CI655302
EST:     GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAG                         CTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAC
genomic: GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
EST: gi|88903805|gb|CI711507.1|CI711507
EST:     GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAG                         CTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
genomic: GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
EST: gi|55415427|gb|CV727803.1|CV727803
EST:     GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAG                         CTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
genomic: GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
EST: gi|88311719|gb|CI574936.1|CI574936
EST:     GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAG                         CTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
genomic: GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
EST: gi|88351412|gb|CI627428.1|CI627428
EST:     GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAG                         CTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
genomic: GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
EST: gi|88735599|gb|CI759107.1|CI759107
EST:     GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAG                         CTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
genomic: GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
EST: gi|66928127|gb|CX114975.1|CX114975
EST:     GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAG                         CTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
genomic: GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
EST: gi|88402595|gb|CI598822.1|CI598822
EST:     GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAG                         CTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
genomic: GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
EST: gi|218481045|gb|FG949218.1|FG949218
EST:     GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAG                         CTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
genomic: GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
EST: gi|218485232|gb|FG957354.1|FG957354
EST:     GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAG                         CTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
genomic: GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
EST: gi|218484368|gb|FG949629.1|FG949629
EST:     GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAG                         CTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA
genomic: GGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAA

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: 62 (upstream exon), 75 (downstream exon)
Score: 72

CAGAACATGCCTAAAATAAAGACAAGCCGTGTCAAATATCCTGGAGGATGGGAGCTTATTGAACCAACTATCCGTGAGTTGGATGCCAAAATGAGGGAAGgtatgacata ... actcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttattgatacttctgctcttatatggatactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA
                               tactaat  putative branch site (score: 72)
                                          tctactc  putative PPT
                              atactaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgacatatgctcccctttcagatgtttattgatacttctgctcttatatggatactaatatcatctactcatgtagCTGAAAATGACACACATGATGGGAAGAGAAAGTGCGAAGCCCTCTGGCCAATTTTCCGTATTTCCCATCAAAGAAGTCGCTACATATATGATCTTTATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT