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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_T07
intron # 3
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
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatgagtataatatatcaagaataaataatgggaagttaaaacttaattgtttacatggtgtggctggtgtttcctctttttttttctcaatcttcagGTATTGTTCTTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTC

- - - - - - - - - - -gaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - catggtg