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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccctttttggaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA

Basic information

species Zea mays
transcript GRMZM2G041181_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 12
--------------------------------------------------------------------------------------------------------gtcagttttctattatcaaccgt------tctaattttcctgaaccaacttcagtgtgacatacttgagccctttttggacc---gcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA
                                                                                                        |  ||| || || ||| || ||       | |  ||||    ||  || |     ||    ||  |||||| ||||   |     |  ||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||||||||| || |||||||| ||| | || || |||||| | |        |
gtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGTGATGCAACTAGGGGTGCTATGCGGGCAGCTTTTTAATTATCAGAAAAGA

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 12
------gtcagttttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccctt-tttggaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTG-TGGTA
       |||  ||   | | | |  |   |  ||| || ||||   |||| ||| |    |  ||||     |  ||  |     |||||||||| || |||||||||||||| ||||| ||||||||||   | |||||||| ||  |||| ||  ||||||  || ||  | |||   |||   |   |
gtttttatcatattagcactgtaacaccaacatattctcttgaagttacttgagtctttt-tgtttgattatgtgcttttaaattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGTGAGGCTGCGAGAGGGACAATGATGGCAGCTCTATAA-CATGGCACTTACA

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA07G31090.3 (Glycine max), 3'ss of exon 11
---------------------------gtcagttttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccc------tttttggaccgc-gtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA
                            |||  ||      ||| |||   | | |||   |||    | |||  |  ||||||| |   | |      | |||||   ||  | |||||||| ||||||||||||||||| ||||| |||||||| |||||||| || || ||  | ||||| |||||||| || ||| | | |        |  | 
gtttgattacacttcttgaactttacaatcatcttaagcacatccacca--ccattttgaatgacatgatttccttacgacatacctctactcactgtttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 10
---gtcagtt-ttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccctttttggaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA
    | | |  | |||   || ||| |  |   ||  ||       ||  |||||    |   |   |  ||  |  |      ||||||||| |||||||||||||| || |||||||||||||||| ||||| |||||| ||  ||   || || ||||| || ||  |                 
gtttttaatagtcctaaactctaccatggtgcattctct----tggctctagtgttttctttgttgacatttaatttat-atacgcagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA----------------

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 12
------gtcagttttctatt--atcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagcccttt-ttggaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTG-TGGTA
       | |  ||   | |  ||| | | |  ||||| |||||||   ||||  || |    |  ||||    ||  ||  |     |||||||||| || |||||||||||||| ||||| |||||| |||   | || ||||| ||  | || ||  ||||||  || ||  | | |   |||   |   |
gtttttataatattaacacttaatctaacttggtaattctcctgaagttacttgtgtctttt-tgtttgactatttgattttatattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGTGAGGCTGCCAGAGGCACAATGATGGCAGCTCTATGA-CATGGCACTTACA

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 13
--------------gtcagttttct--attatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccctttttg---gaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA
               ||| |||| |     |         || |      |||   ||| | |       | |  |   |  ||||||   |   || | |||||||| || |||||||||||||| ||||| |||||||| ||||||||||  || ||  | || || ||| |||| || |||   | |             
gtttgaatatacatctcaatttttttggaaagtggaaacacttagcactttgactgaacataaccaaagtacatgttcactttttttgtttgtttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCATTGAGGGCTGCAAGATGA-------------

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 11
-------------------------------------gtcagttttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccctttttggaccgc-gtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA
                                     |    |   | |  ||      | | |   || |   |  || | |    |  || |||       | |||||   ||  | |||||||| |||||||||||||| || ||||| ||||| || |||||||| || || ||  | ||||| ||| |||| || ||| | | | |     ||  | 
gtttgactacacttcttgaactttccaatcatcttaagcacatgcaccagcattttgaatgccatgatttccttatgaattaccacatacca-actcactatttctttggtttgctatacagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGGGAGGCCGCAAGGGGAGCACTGAGGGCTGCAATATGATTCATCAGTCTTG

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA15G07480.2 (Glycine max), 3'ss of exon 11
----------------gtcagttttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagcccttt-ttggaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAA-GTGTGGTGTGGTA
                |    ||||     |       | || |      |||   ||| | |         |  |   |  ||| || |   || | |||||||| || |||||||||||||| ||||| |||||||| ||||||||||  || ||  | || || |||||||| |  ||| | | |    |    | || 
gttcgaatatacatctgaatatttttggaaagtggaaatacttagcactttgactgaacataaccaaagttaatgttcactttttgtttggttgcatacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCAATGAGGGATGCAATATGATAAATTACTTTGT-

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT1G03550.1 (Arabidopsis thaliana), 3'ss of exon 11
--------------gtcagttttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccctttttggaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA
                 | |     |||    | |  | ||| |  | |||| | |  |   | |   |  | ||| |      |   |  | | |||||||| ||    |||||||| || ||||| || |||||||||||||||||||| || || |      |  |||     ||| | | |           | 
gtttctcaacttcttctactccagaatttatcagcactgtaaatcacttgaatccatctgtttttctaacccatga-cgtgcaatactcgactttcagCAAGTATATGCATACTTCCGAGGGAGTGGCAAAGCTGCAGAGATGAAGCGTGAAGCTACAAAATCGACCTTGATGCGTGCACTATGAAGAAATCACTCTT

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 11
--------gtcagttttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccctttttggacc--------gcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA-
        ||| | |||||| |        |||||  |         | ||| ||   ||   |  |  | | || ||||  |            |||||||||| |||||||||||||| || ||||| ||||||  |||||| |||||||||||| | || ||  |  | |     ||||||| | ||||    ||   
gttcagtagtctgatttctagttcttctgcttctatctccagcacttctactgcatcttggtttcttctaactctctttgttctcaatcccaatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGTGATGCGGCAAGAGGGACTGTAATGCAAGCATTTTGA-TGTGCCACGGATG

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
--------------gtcagttttctattatca-----accgtt-ctaattttcctga----accaac--ttcag-tgtgacatacttgagccctttttggacc--gcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA
                |  ||    || ||||     | | |  |||  | | || |    |  ||   | ||| | |     |||    |  || ||  |||  |  |||||||||| || ||||||||||| || ||||| || || || |||||||||||||| ||  | || || || ||||| || ||||| ||||  ||   |    
gtccaacttctctttcccattcctaataatcacggaaagcatagctacctctgctaataggatgaatcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC

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|60342784|gb|DN209757.1|DN209757
EST:     GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG                         CAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
genomic: GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
EST: gi|18384947|gb|BM418146.1|BM418146
EST:     GATTTGGACTGTTCTGTCTGGAATCATTGCTCAGCATCTGGGTCATCCAG                         CAAGTGTACATGTTCTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
genomic: GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
EST: gi|149103005|gb|EE288366.2|EE288366
EST:     GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATTTGGGTCATCCAG                         CAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
genomic: GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
EST: gi|18384946|gb|BM418145.1|BM418145
EST:     GATTTGGACTGTTCTGTCTGGAATCATTGCTCAGCATCTGGGTCATCCAG                         CNAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
genomic: GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
EST: gi|33771071|gb|CF273365.1|CF273365
EST:     CTGGAATCATTGCTCAGCATCTGGGTCATCCAG                         CAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
genomic: CTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
EST: gi|76018526|gb|DT945696.1|DT945696
EST:     GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG                         CAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
genomic: GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
EST: gi|29543932|gb|CB604312.1|CB604312
EST:     GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG                         CAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
genomic: GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
EST: gi|78023022|gb|DV491409.1|DV491409
EST:     GATTTGGACTGTTCTGTCTGGAATCATTGCTCAGCATCTGGGTCATCCAG                         CAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
genomic: GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
EST: gi|67033086|gb|CO461835.1|CO461835
EST:     GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG                         CAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCANAGATGAAGCGT
genomic: GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
EST: gi|110944605|gb|EE164762.1|EE164762
EST:     GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAG                         CAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT
genomic: GATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGT

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: 49 (upstream exon), 45 (downstream exon)
Score: 162

ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 209

ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 79

ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 413

ATATTCTACTTTGTTGGATTTGGACTGTTCTGTCTGGAATCATTGCTTAGCATCTGGGTCATCCAGgtcagttttc ... ccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctgaaccaacttcagtgtgacatacttgagccctttttggaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA
                                     ttttt  TA-rich tract