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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtggtaccagattgatcacaatttttcactcctttggtttcagcctactggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG

Basic information

species Zea mays
transcript GRMZM2G064023_T04
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
gtaatgtggtaccagattgatcacaatttttcactcctttggtttcagcctactggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
||||||    || ||||||||||  |||  | ||   |||   | || | || ||| ||  ||       | ||| |||| ||| |  ||||||| ||||| ||||| |||||||||||||||||||||||| ||||||||||||||||| |||||||||| ||
gtaatgc--cactagattgatcatgattgct-accgttttatgtccatcttattggctaaaaagtgacaacattgtccatatttcc--agGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
gtaatgtggtaccagattgatcacaatttttcactcctttggtttcagcctactggttatgaacaccactctttgcccatg------------------ttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
||||||   ||| ||||||||||  | || |  |||||||  || | ||    |   | |     |  ||| ||| | | |                    || ||||||||| ||||| ||||| ||||||||||||||||| |||||| | ||||||||||||||| |||||||||| ||
gtaatgc--tactagattgatcaataattattgctcctttaattacggctccttcagtttacttccatctcattggctaagaaataagaacatccttcacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 17
----------gtaatgtggtaccagattgatcacaatttttcactcctttggtttcagcctactggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
            ||   | || |||||  |        | ||   |  || |||  |   || |  | ||       |   |  |       |     |||| || || || ||||| |||||||||||||||||||||||  | |||||| | | ||| ||| |||| | |  
tcatacacattaaaccggataacagatgtactcattgctctcttgctattagttgtaatttattcctgatacgactgaacttgagttttaaatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA15G42300.1 (Glycine max), 3'ss of exon 17
gtaatgtggtaccagattgatcaca-----atttttcactcctttggtttcagcct--actggttatgaacaccactctttgcccatgttttct------cagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
 | ||        | |  ||| |||     | |  |  |||  | | | | || |   | |  ||    | || |||     |    ||||||        |||| || || || ||||||||||||||||| |||||||||||  | |||||| ||| ||| ||| |||| | |  
-tgatacacattaaaacggataacagatgtactcattgctctctagatattagtcataatttattcctgatacgactg--aacttgagttttcaacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaatgtggtaccagattgatcacaatttttcactcctttggtttcagcctactggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
||| |       |  ||| ||  || | |   ||    ||   |        |||||| |    | |     |||    || | | ||||||||||||||||||||| || ||||||||||| || |||||  | |||||| ||| ||| ||| | |||||| |
gtactacttatactcattcatttca-tgtgctaccagattttctgattttctctggttttatgaatc-----ttgaaattgctgtatcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 17
----------------------------------------------------------gtaatgtggtaccagattgatcacaatttttcactcctttg-gtttcagcctactggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
                                                            ||     ||||    || |      || | | ||  ||| |  |||   |  |  |||    |   |  |  ||      || |  ||||| |||||||||||||| |||||||||||||||||||| || ||||||||||||| ||| ||| | |||||| |
gtagtatctctatccttcgtttaccatggtgatccttcaatattccaccaacaactccacaacaccttacctacatgctaggggcttatgaatctcttgcgaatcaattttttatttacttgcga-atccgatgatggc-ttgttacagGTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
----gtaatgtgg-taccagattgatc----acaatttttcactcctttggtttcagccta-ctggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
    | ||  ||  ||| ||| |  |     | ||  |||  || |  || |  | |   |  |     |||       |              |   |||| || ||||| ||||| ||||| |||||||||||||| || ||||||||||| |||||  ||   ||||||||
ttctgcaacatgcctactagaattctgtaaaataaactttggcttcagtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
lower sequence: PP1S37_33V6.1 (Physcomitrella patens), 3'ss of exon 11
--------------------------gtaatgtggtaccagattgatcacaatttttcactcctttggtttcagcctactggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
                           | | || ||  | |       | ||  || |||| |||| |        |    ||  |    ||   | || |     |  |  ||||||||||||||| ||||| ||||| ||||||||||| || ||  ||||  |  |||  ||  |    |||     
gtaagtttcgaaggtttaagaactttatgaagtagtcgccgtcaagaaaaaaaattccacttcttttgaagtcattttgaagtctt----acttgtgttcgtgtgcgagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
lower sequence: PP1S163_94V6.1 (Physcomitrella patens), 3'ss of exon 15
-----------------------------------------------------------------gtaatgtggtaccagattgatcacaatt----tttcactcctttggtttcagcctac--tggttatgaacaccactctt-tgccca-tgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
                                                                 ||||    | |||    |  ||  |||     ||  | ||  ||  |   ||  |     | |  |||  |    ||   |||  | | ||||  ||||| || ||||| ||||||||||| |||||||| |||||||| |||||  | |||| ||| ||    |||     
gtacggtttttttatgtctgtccaccacaataggcctagatattcaatttgaatttaacttgggagtaa-aaagcacccagctactcggaataatggttgtagtcacttcatgcaagattgtaacgctcgtgactagtcttccagtgcataattttttgacagGTAAAAAACCCATGGCCGAATGTAGATGCTCATAGTGGAGTATTGCTTCAACACTATGGTCTGAAAGAACAGAA

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|211314254|gb|FK994154.1|FK994154
EST:     TGTCCTTTTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG                         GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
genomic: TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
EST: gi|6020672|gb|AW065480.1|AW065480
EST:     TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG                         GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
genomic: TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
EST: gi|5847106|gb|AW000185.1|AW000185
EST:     TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG                         GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
genomic: TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
EST: gi|67022591|gb|CO451340.1|CO451340
EST:     TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG                         GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
genomic: TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
EST: gi|32859372|gb|CD999053.1|CD999053
EST:     TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG                         GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
genomic: TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
EST: gi|71450119|gb|DR831169.1|DR831169
EST:     TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG                         GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
genomic: TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
EST: gi|4776524|gb|AI665527.1|AI665527
EST:     TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG                         GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
genomic: TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
EST: gi|76284364|gb|DV023932.1|DV023932
EST:     TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG                         GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
genomic: TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
EST: gi|6952534|gb|AW424602.1|AW424602
EST:     TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG                         GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGCGGAGTTTTGCTGAAC
genomic: TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
EST: gi|31361873|gb|CD446230.1|CD446230
EST:     TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG                         GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
genomic: TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
EST: gi|149082724|gb|EE171942.2|EE171942
EST:     TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAG                         GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC
genomic: TGTCCAAGTTATATGAAGTCGTACCTCCGATCCTCACTGAGCTAGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttggtttcagcctactggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
                                            tgttttctc  CT-rich tract
                     ttatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtggtaccagattgatcacaatttttcactcctttggtttcagcctactggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC