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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatgagtataatatatcaagaataaataatgggaagttaaaacttaattgtttacatggtgtggctggtgtttcctctttttttttctcaatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTC

Basic information

species Zea mays
transcript GRMZM2G067985_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067985_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g01600.2 (Oryza sativa), 3'ss of exon 3
------aaaatgagtataatatatcaagaataaataatgggaagttaaaacttaattgtttacatggtgtggctggtgtttcctctttttttttctcaatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTC-
           ||    | | | || ||     |  |     || |||   |  |    | | ||| | |   | | |   | | | ||| | |     ||| |||||||||||||| || |||||||||||||| |||||||| ||||||||||| ||||||||||| ||||||||||||||||| ||||||||||| ||||||| 
aagctacctgcgaccccattgtgtccaggcctga--acaaacagctaactgtcgacaagtaa-atgttttatttagaggagcttatgtttctctgc---tctgcagGTATTGTTCTT-GATTCTGGTGATGGTGTCAGCCACACAGTGCCCATTTATGAAGGATATGCGCTTCCTCATGCCATTCTCCGTTTGGATCTGGCTGGTCG

upper sequence: GRMZM2G067985_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G05570.1 (Glycine max), 3'ss of exon 3
aaaatgagtataatatat-caagaataa-ata-atgggaagttaaaacttaattgt---ttacatggtgtggctggtgtttcctcttttttt-ttctcaatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTC-
        |   | |  | ||||| |   ||| |   | | ||  |  |||||| |      |||  | |   |  || ||  |||| || | ||   | |   |||||||||| ||| || ||||||||||||||||||||||| |||||||| || ||||| ||||| ||||||||||| |||||||| ||||| |||||||| | 
-------attccacacgtacaagagtgggatatacatgcatttctacattaattatgaccagcattatttccttattggtttgtcttgttatgttggtattaaacagGTATTGTGCTT-GATTCTGGTGATGGTGTGAGCCACACGGTGCCCATATATGAAGGGTATGCTCTTCCTCATGCAATTCTTCGGTTGGACCTTGCTGGCCG

upper sequence: GRMZM2G067985_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 3
aaaatgagtataatatatcaagaataaataatgggaagttaaaacttaattgtttacatggtgtggctggtgtttcctctttttttttct--caatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTC-
 | ||    || |  |   |   | |  || |   |  ||||  | | |        ||  | |   |  | | |  ||||| || |  |  || |   |||||||||| ||| || ||||||||||||||||||||||| || ||||| || ||||| ||||| ||||||||||| |||||||| ||||| |||||||| | 
-acatatacatga-gtgggatatacatgtatttccacattaattcctcacgaccagtattatttccttattttcttgtctttgttatgttggcattaaacagGTATTGTGCTT-GATTCTGGTGATGGTGTGAGCCACACAGTTCCCATATATGAAGGGTATGCTCTTCCTCATGCAATTCTTCGGTTGGACCTTGCTGGCCG

upper sequence: GRMZM2G067985_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G15480.1 (Glycine max), 3'ss of exon 3
aaaatgagtataatatatcaagaataaataatgggaagttaaaacttaattgtttaca-tggtgtggctggtgtttcctctttttttttctcaatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTC-
                        || || |      ||    | | | |  |||| | |    | | |    || |||   |   || ||       ||||||||||  || |||||||||||||||||||| |||||||| || || || || || ||||| || || |||||||| |||||||||||||| ||||||| 
-------------------gtttgtatatcaccatctgtcttgattcattcttttataatcacattgtt--ctttccctgaatcaattccttttaaaacagGTATTGTA-TTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCTGGTCG

upper sequence: GRMZM2G067985_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 2
aaaatgagtataatatatcaagaataaataatgggaagttaaaacttaattgtttaca-tggtgtggctggtgtttcctctttttttttctcaatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTC-
                        || || |      ||    | | | |  |||| | |    |   |  |        |   ||  | ||||    ||||||||||  || |||||||||||||||||||| |||||||| || || || || || ||||| || || |||||||| |||||||||||||| || |||| 
-------------------gtttgtatattaccatctgtcttgattcattcttttataatcacatcattctttccctgaatcaattcctttcaaa--acagGTATTGTG-TTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCAGGTCG

upper sequence: GRMZM2G067985_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G39380.2 (Glycine max), 3'ss of exon 3
aaaatgagtataatatatcaagaataaataatgggaagttaaaacttaattgtttacatggtgtggctggtgtttcctctttttttttctcaatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTC-
             | |||    |   |    |   || | | |  ||  |  |  |||| ||    ||     |   ||   |  ||||| ||    ||||||||||| || |||||||| |||||||| || ||||||||||| || || || || ||||| || |||||||||||||||||||||||||||||||| | 
----------gtttgtatttgtatccatctgtttcaattcatagttttgtcatc-acattgt---tctttccctgaatcaaatactttctgaa---acagGTATTGTT-TTGGACTCTGGCGATGGTGTTAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTTCGTTTGGATCTTGCTGGCCG

upper sequence: GRMZM2G067985_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 3
aaaatgagtataatatatcaagaataaataatgggaagttaaaacttaattgtttacatggtgtggctggtgtttcctctttttttttctcaatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTC-
             | ||   |     |    |   || |    |||   |||| | ||   |||      |  ||        | ||| | ||   |||||||||||| || |||||||||||||||||||| ||||||||||| || || || || ||||| || |||||||||||||| ||||||||||||||||| | 
----------gtttgtacttatttccatctgtcttaattc---actcctttgtcttcacattgt--tctatccttgaatcaaatctttttgaa---tcagGTATTGTT-TTGGACTCTGGTGATGGTGTGAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTCCGTTTGGATCTTGCTGGCCG

upper sequence: GRMZM2G067985_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 3
aaaatgagtataatatatcaagaataaataatgggaagttaaaacttaattgtttacatggtgtggctggtgtttcctctttttttttctcaatctt---cagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTC-
                 | |    | ||   |    |   ||  || | || | |  ||  | |  || || ||| ||     |  |||||  | |    |||||||||| ||  || |||||||||||||||   ||||||||||| || ||||| || ||||| ||||||||||| || |||||| | |||||||| |||| 
----------------gttagttcttaactctaaacatccaagtctgagttatat-tatcttcttacttgtatttacttaaagtcgttctctttttgtaacagGTATTGTGCTC-GATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACGAGGGGTATGCTCTTCCTCATGCTATCCTTCGTCTTGATCTTGCGGGTCG

upper sequence: GRMZM2G067985_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 4
aaaatgagtataatatatcaagaataaataatgggaagttaaaacttaattgtttaca--tggtgtggctggtgtttcctctttttttttctcaatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTC-
       || |  |||   ||   |     || |||| ||  |  ||  || | |     | |||| ||  | |||    |||  |  ||     |    ||||||||| ||  || ||||||||||||||||| ||||||||||| ||||| ||||| ||||| ||||| ||||| || |||||| | || |||||||| | 
-------gt-tcgtattaaaatctttttggattggaattttcatttttcttttctgttgttagtgtagcctgagttctaacttgctcctt-----tgactagGTATTGTGCTG-GATTCTGGTGATGGTGTGAGTCACACTGTGCCAATTTATGAAGGTTATGCACTTCCCCATGCTATCCTTCGTCTTGACCTTGCTGGACG

upper sequence: GRMZM2G067985_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 3'ss of exon 2
aaaat--gagtataatatatcaagaataaataatgggaagttaaaacttaattgtttacatggtgtggctggtgtttcctctttttttttctca-atcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTC-
||| |   || ||  | |    || ||   |||  |     ||  | ||  || |   | || | |   |  | ||| ||    ||||||      |    ||||||||| ||| || |||||||||||||| ||||| || ||||| || || ||||||||||| ||||| ||||| || ||||| || || |||||||||| 
aaatttcaagaattttttcctcagtattggtaactgccgactatgattttcttat---cctgttctttgttatatttactgaagttttttggtgtgtgaaaagGTATTGT-CTTGGATTCTGGTGATGGTGTCAGCCATACAGTGCCAATCTATGAAGGATATGCTCTTCCACATGCAATCCTTCGATTAGACCTTGCTGGTCG

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|211471833|gb|FL184449.1|FL184449
EST:     TATGCTAGTGGGCGTACTACTG                         GTATTGTTC-TTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
genomic: TATGCTAGTGGGCGTACTACTGgtatgacctg ... caatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
EST: gi|211469310|gb|FL184438.1|FL184438
EST:     TATGCTAGTGGGCGTACTACTG                         GTATTGTTC-TTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
genomic: TATGCTAGTGGGCGTACTACTGgtatgacctg ... caatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
EST: gi|31355571|gb|CD439928.1|CD439928
EST:     TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTTCTT-GACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
EST: gi|67031467|gb|CO460216.1|CO460216
EST:     TGTTGCAATCCAAGCAGTGCTCTCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTTC-TTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
EST: gi|211466785|gb|FL184425.1|FL184425
EST:     TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTTCTT-GACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
EST: gi|5325045|gb|AI783236.1|AI783236
EST:     GCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTTC-TTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
genomic: GCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
EST: gi|211466786|gb|FL184426.1|FL184426
EST:     TATGCTAGTGGGCGTACTACTG                         GTATTGTTC-TTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
genomic: TATGCTAGTGGGCGTACTACTGgtatgacctg ... caatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
EST: gi|211471834|gb|FL184450.1|FL184450
EST:     TATGCTAGTGGGCGTACTACTG                         GTATTGTTC-TTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
genomic: TATGCTAGTGGGCGTACTACTGgtatgacctg ... caatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
EST: gi|5846857|gb|AI999940.1|AI999940
EST:     GCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGNTC-TTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
genomic: GCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
EST: gi|116815584|gb|EC858264.1|EC858264
EST:     TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTTC-TTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
EST: gi|62550511|gb|DN830931.1|DN830931
EST:     GTGGGCGTACTGCTG                         GTATTGTTC-TTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
genomic: GTGGGCGTACTACTGgtatgacctg ... caatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
EST: gi|23357518|gb|BU645167.1|BU645167
EST:     TGGTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTG                         GGATTGGTC-TTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattgtttacatggtgtggctggtgtttcctctttttttttctcaatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTC
 acttaat  putative branch site (score: 4)
                         tgtttcctcttttttt  putative PPT
                                  tttttttttctcaat  TA-rich tract