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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtggtccattttgctgccttctatttcagcttatgttatccccatggcttcattgtctgtttaagaaatcctctacatttattctgaatgtagggcagCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGATCAGTACAACGGCTTTAACCTTATATTGGCTGATGTGAACTCAGGAACCATGGTT

Basic information

species Zea mays
transcript GRMZM2G003057_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003057_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g47680.1 (Oryza sativa), 3'ss of exon 1
gagtggtccattttgctgccttctatttcagcttatgttatccccatgg---cttcattgtctgtt--taagaaatcctctacatttat---tctg-aatgtagggcagCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGATCAGTACAACGGCTTTAACCTTATATTGGCTGATGTGAACTCAGGAACCATGGTT
   |      || | | ||  ||  | | || |||  ||    | || |   |||  ||   | ||  |||    || | ||| |  ||   |||   ||  |||| | ||  ||||| |||||||||||   |||||| || |||||||||||||||||||| |||||||||||| |||||||||||||| | || ||||  |     
--attacatgttctacagc--tccttcttagattagcttcctacaattgatccttgcttaattattgataatgtttcttttacttcaatgaatctatgatacagGGAAACCAATGTCCGTTGGAGTATGCGGAAGAAATAGCCAAGGAAGCAGATCAGTACAATGGCTTTAACCTTGTATTGGCTGATGTGCAGTCGGGAAATA-----
















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|211421544|gb|FL418414.1|FL418414
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211421544|gb|FL418414.1|FL418414
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211421544|gb|FL418414.1|FL418414
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|93284444|gb|EB676708.1|EB676708
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|93284444|gb|EB676708.1|EB676708
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|93284444|gb|EB676708.1|EB676708
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|149100496|gb|EE186576.2|EE186576
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGGGCAG                     
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCT--A---CAGgttcggcctt ... tgtagg
EST: gi|211127336|gb|FL391795.1|FL391795
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211127336|gb|FL391795.1|FL391795
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211127336|gb|FL391795.1|FL391795
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211509432|gb|FL413813.1|FL413813
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211509432|gb|FL413813.1|FL413813
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211509432|gb|FL413813.1|FL413813
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211256544|gb|FL390497.1|FL390497
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211256544|gb|FL390497.1|FL390497
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211256544|gb|FL390497.1|FL390497
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211484497|gb|FL376552.1|FL376552
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211484497|gb|FL376552.1|FL376552
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211484497|gb|FL376552.1|FL376552
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211242704|gb|FL378106.1|FL378106
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211242704|gb|FL378106.1|FL378106
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211242704|gb|FL378106.1|FL378106
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         G
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcag-
EST: gi|211394987|gb|FL376971.1|FL376971
EST:     CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAG                         CCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGATCAGTA
genomic: CTCTGATCGGGGCCAAGACCAGAGGACAGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcagCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGATCAGTA
EST: gi|60340900|gb|DN207873.1|DN207873
EST:     AGCTCCCGGTCAGGTTTCTACAG                         CCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGATCAGTA
genomic: AGCTCCCGGTCAGGTTTCTACAGgttcggcctt ... tgtagggcagCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGATCAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggcttcattgtctgtttaagaaatcctctacatttattctgaatgtagggcagCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGATCAGTACAACGGCTTTAACCTTATATTGGCTGATGTGAACTCAGGAACCATGGTT
                tttaagaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtggtccattttgctgccttctatttcagcttatgttatccccatggcttcattgtctgtttaagaaatcctctacatttattctgaatgtagggcagCCTTTGTCCATTGGAGTATGCCACAGAAATTGCAAAGGAAGCAGATCAGTACAACGGCTTTAACCTTATATTGGCTGATGTGAACTCAGGAACCATGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - ttgctgc
- - - - - - - - - - - - - - - gcttatg
- - - - - - - - - - - - - - - - - - - - - -ccatggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgaa