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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG

Basic information

species Zea mays
transcript GRMZM2G391042_T01
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagt-tcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
                                                        |   ||       ||| | | | |  ||||  || ||| || ||   |||     |||||||| || |||  |    |  | |||  | ||  |||||  |   |||||||||| ||||| || ||||| || ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||| ||||||||||||
--------------------------------------------------------gtttatctctcgactaatgttccatcatgtt-ttgaaagaaacaatcttc-----atgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG

upper sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
                                   || | | |  | |     ||  ||||   | ||| | ||||  | || ||||  ||        | ||| ||| | ||||   |  ||    |||        |||||             |  |||| |||||||||||  ||||||| || || || || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| || || |||| |
-----------------------------------ctattaga--atctattgttcagacacacattttttggttcaaattaggtaaactagtt---tttgttttcatggttgtttttgtgactctattt--------ttgag-------------tttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
                                |   || ||| | |   | ||| ||   |   | ||| | ||||  | ||||| |  ||        | ||| ||| | |||    |  || ||| || || |   ||                   |||| |||||||||||  ||||||| || || || || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| || || |||| |
--------------------------------tctattagaatcta---ttgttctg---acacattttttggttcaaattatgtgaactagtt---tttgttttcatggttgtgtttgtgac-tctatttttggagttt-------------------agGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 24
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
                                                     |   |   |||||| ||    | | |||    |  ||         |  |     ||      |      ||  |||  | ||| ||    |  | |      |  |||| ||||| |||||| ||||||| || || || || |||||||| || ||||| || ||||| ||||| ||||||||||||||||| || || |||| |
-----------------------------------------------------taaaggtttgaactatc---attccaatgcagatgtttt-----tgttctaatgcagtaaactagcttttattcttttcttgtaattctatacatttttggaatatagGCCGATATAGGTCTAGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCCGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 26
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
                                                          |  |||| |||  | ||| | || |  ||  || |         ||  ||  || | |     | |  |  |   ||| ||| |  |  | || || ||  |||||||||||||||| || ||||| || || ||||| |||||||| || || ||||| |||||||| ||||||||||| || ||||| || || || | |
--------------------------------------------------------aaagttgaaatttaaaattcattat-taaaacctagagtttatcaattatattaatttccttattatagttgatac-agtgctttacta-ttatgtaattt--agGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAG

upper sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 24
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
                                  |  ||  ||| |   || |||       | | ||| |   | ||||| |      ||||| | |    ||  ||                ||| || ||   | |  | | | | || ||  |  |||| ||||| |||||  ||||||| || || || || |||||||| || ||||| |||||||| ||||| ||||||||||||||||| || || |||| |
----------------------------------aggtttgaacta---tcatttcaatgcaggagtttttg--ttctaatgtag----taaactaactagcttttat----------------tctgtttttgtaattctatacattttggaa--tatagGCCGATATAGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 26
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgtt-ttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
                                       |  ||||    ||    |||| || ||    || |   | || ||||||||| |     ||| |||  ||    ||| |   ||  |  |||  || ||            || || ||  |||||||||||||||| || ||||| || || ||||| |||||||| || || ||||| |||||||| ||||||||||| || ||||| || || || | |
--------------------------------------gggtaccaaatccgaaactggaaataaa----ctgggatcaaaaatgtaattttac----catttttttattatagtttatacaatgt--tttactatta------------tgtaattt--agGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAG

upper sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
lower sequence: AT5G57110.1 (Arabidopsis thaliana), 3'ss of exon 26
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaa---acttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
      | |  ||| | |     |||||  | | |   ||     |||  | | |   ||   || |||||  |  | ||   ||| |||   |   | | ||| |  ||       |  |  ||||    || ||  |  | |   | |||    | ||||||||||||||||||||  | ||||| ||    ||||| ||||| |||||||||||||| || || || |||||||||||||| ||||| || || || | |
------gtatagtaatttactgaaatttaaactgataatgtcgaaagctacatct--aactgaaagtttcttttggccaa---gtattttg--cctacgtttttactcagcgagcggatcattatctc--attggtgtt--aaattttttgagtgtatttgcagGCAGATATTGGTCTTGCTATGGGAATAGCAGGAACAGAAGTGGCTAAGGAGAGTTCGGACATCATCATCTTGGATGACAACTTTGCTTCAGTTGTCAAG

upper sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 24
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
                                                                         |  |||| |  |         | | ||  |    |   |||       | ||||   | |  | |||  |   || || |   |  |||||||||| ||||| || ||||| ||    |||||||||||||| || ||||||||||| || ||||| ||||||||||||||||| || || || | |
-----------------------------------------------------------------------gttctctaacaattctacaggttatgtattatgtgttgtgtgtcatctccaaatct---gatttttcttttgttgctttgga--ctatagGCAGATATAGGTCTCTCTATGGGTATATCAGGAACTGAAGTTGCAAAAGAGAGTTCTGACATCATTATTTTGGATGACAATTTTGCTTCAGTAGTAAAG

upper sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
                                                   |||    ||||  || |||      |  || |||||  |  | ||  |   |   || || | ||     |||  || |||          |   | |   ||||| ||||||||||| |||||  ||||||| || || || || |||||||| ||||| |  || || || ||||||||||||||||| ||||  || || |||| |
---------------------------------------------------gttcaatacatttacattcc----tcgtatgtgtaagctttaaaaatacactgttattgaggatc-----acactttctgt----------gttgccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG

upper sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacat---cttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
                                                      |   | | |   |||||| |  ||  ||| |||       || ||| |||  |||  |   |        |   | ||| ||  | |||       | || |  ||  ||||||||||||||||  ||||||| |||   ||||| || ||||| || ||||| ||||| || ||||||||||||||||||||||| || || || | |
-----------------------------------------------------ctcaaatagg---tttctaatatcttttatataaa------aaacatttttttatattttccccgctcttgttcgccttttttttttcttttttttttttggacttt--agGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG

upper sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 26
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
                                                    || |||   |  | |||   | |  |  | |   || |     ||||  ||   |  | ||||        ||  ||  | ||    |   |   |||     ||| |||||||||| ||||| || ||||| ||||| |||||||||||||| || || || || || || |||||||||||||| || |||||||| || || | |
----------------------------------------------------ttatggctgtagagttt--ggatgttgtttttccatct---tcagcaggttcataatgttgtttctttgtaatgattgatcaggttgtatcattttcta----ttgtagGCAGATATAGGTCTCTCTATGGGCATTCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGACATCATTATCTTGGATGATAACTTTGCCTCAGTTGTAAAG

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|67018575|gb|CO447324.1|CO447324
EST:     TTGTTGCTGTTACTGGAGATTGCACAAATGATGCCCCAGCACTGCCTGAG                         GCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAG
genomic: TTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggac ... aaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAG
EST: gi|60350742|gb|DN217715.1|DN217715
EST:     TTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAG                         GCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAG
genomic: TTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggac ... aaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAG

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 4 RNA-Seq libraries.


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 35

ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCACGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggac ... aaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG


Block sizes: 32 (upstream exon), 34 (downstream exon)
Score: 7

ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCACGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggac ... aaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 22

ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCACGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggac ... aaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCACGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggac ... aaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
                    ttttgtta  TA-rich tract