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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttccccttctattcttctctgctgtgcgctgctgctgtcccggttcgggaggttgaatgctgaggggaatgctaataccaacaaaataatagggtaaggtctttgatttcatcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCCTCGAATCATCGCAGAAGTTGCTAGATTCAAGCCTGACATTATTCACGCC

Basic information

species Zea mays
transcript GRMZM2G100652_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100652_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g01030.1 (Oryza sativa), 3'ss of exon 2
gtgagttccccttctattcttctctgctgtgcgctgctgctgtcccggttcgggaggttgaatgctgaggggaatgctaataccaacaaaataatagggtaaggtctttgatttcatcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCCTCGAATCATCGCAGAAGTTGCTAGATTCAAGCCTGACATTATTCACGCC
                              |   |  |  | |     |    |      | || |||  |    ||  | | || ||   |    |       |  ||   || || |||||   ||||| ||||| ||||| || |||||||| || || || ||||| |||||||| || |||| ||||||||||||||| ||||||||||| |||||||||
------------------------------gtagtattaatataataatatatggacgccattgttgacagtc-cgccgacagcagcatttttgctgacatgtcttatttgattgattccagC---TTCCCCTGCCCGTGGTACCAGAAGGTTCCACTTTCACTAGCCCTAAGTCCTCGGATTATCGGAGAAGTTGCTAGATTTAAGCCTGACATCATTCACGCC

upper sequence: GRMZM2G100652_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA03G14200.1 (Glycine max), 3'ss of exon 3
gtgagttccccttctattcttctctgctgtgcgctgctgctgtcccggttcgggaggttgaatgctgaggggaatgctaataccaacaaaataatagggtaaggtctttgatttcatccca-gcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCCTCGAATCATCGCAGAAGTTGCTAGATTCAAGCCTGACATTATTCACGCC
                        |  ||| |  |||   | ||    ||        ||| ||||      |    |  | |  || ||  |      |     |    |  |      | ||||||||||||| ||||||||||||||||| || || ||  |||| || |||||  |||| ||  | |  ||||||   || ||||||||||| || || || 
------------------------tattgtac-ttgccaatatcttc-tttaaacttatgattgctaccacaaccattgcttcgtacgaatgatcttcatttaaacaaaaacattgaaaaatgcagCTTCCCTTGTCCCTGGTATCAAAAGGTGCCTCTCTCTTTGGCACTTAGTCCAAGAATAATTTCTGCGGTTGCTGAGTTTAAGCCTGACATAATACATGCA

upper sequence: GRMZM2G100652_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G27840.1 (Glycine max), 3'ss of exon 3
--gtg-agttccccttctattcttctctgctgtgcgctgctgctgtcccggttcgggaggttgaatgctgaggggaatgctaataccaacaaaataatagggtaaggtctttgatttcatcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCCTCGAATCATCGCAGAAGTTGCTAGATTCAAGCCTGACATTATTCACGCC
   || | || ||  | | |||||    | | || | |||| |     |  ||      | |   | || | |   ||  | ||   ||||||| || |  | ||                   ||||||||||||| ||||||||||||||||| || || ||  |||| || |||||  |||| ||  | |  ||||||   || ||||||||||| || || || 
tattgtaattgccagtatgttctttaaagttatg-gttgctaccacagccatt------gcttcgtactaatg---atcttcatttaaacaaaa-aacaatgaaaat-----------------gcagCTTCCCTTGTCCCTGGTATCAAAAGGTACCCCTCTCTTTGGCACTTAGTCCAAGAATAATTTCTGCTGTTGCTGAGTTTAAGCCTGACATAATACATGCA

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|67042909|gb|CO469164.1|CO469164
EST:     GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAG                         CTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
genomic: GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAGgtgagttccc ... atcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
EST: gi|78076032|gb|DV504466.1|DV504466
EST:     GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAG                         CTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
genomic: GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAGgtgagttccc ... atcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
EST: gi|211101764|gb|FL133078.1|FL133078
EST:     GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAG                         CTTCCCTTGCCCCTGGTATCAAAGAG-TTCCGCTGTCGCTGGCCCTCAGTC
genomic: GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAGgtgagttccc ... atcccagcagCTTCCCTTGCCCCTGGTATCAAA-AGGTTCCGCTGTCGCTGGCCCTCAGTC
EST: gi|87156413|gb|DY401202.1|DY401202
EST:     GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAG                         CTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
genomic: GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAGgtgagttccc ... atcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
EST: gi|211101762|gb|FL133076.1|FL133076
EST:     GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAG                         CTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
genomic: GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAGgtgagttccc ... atcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
EST: gi|26560034|gb|CA832269.1|CA832269
EST:     GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAG                         CTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
genomic: GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAGgtgagttccc ... atcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
EST: gi|91869857|gb|EB400576.1|EB400576
EST:     GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAG                         CTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
genomic: GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAGgtgagttccc ... atcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
EST: gi|148981111|gb|EE027429.2|EE027429
EST:     GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAG                         CTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
genomic: GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAGgtgagttccc ... atcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
EST: gi|22935606|gb|BU571881.1|BU571881
EST:     GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAG                         CTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
genomic: GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAGgtgagttccc ... atcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
EST: gi|89762164|gb|DY689888.1|DY689888
EST:     GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAG                         CTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
genomic: GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAGgtgagttccc ... atcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC
EST: gi|86473030|gb|DY239400.1|DY239400
EST:     GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAG                         CTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCACCCC
genomic: GAGGGCGTGCCTCAGGAATTCCACGGAGCCAAGCTAATTGGCTCATGGAGgtgagttccc ... atcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatgctaataccaacaaaataatagggtaaggtctttgatttcatcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCCTCGAATCATCGCAGAAGTTGCTAGATTCAAGCCTGACATTATTCACGCC
                                         tttcatccc  CT-rich tract
              aacaaaataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttccccttctattcttctctgctgtgcgctgctgctgtcccggttcgggaggttgaatgctgaggggaatgctaataccaacaaaataatagggtaaggtctttgatttcatcccagcagCTTCCCTTGCCCCTGGTATCAAAAGGTTCCGCTGTCGCTGGCCCTCAGTCCTCGAATCATCGCAGAAGTTGCTAGATTCAAGCCTGACATTATTCACGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT