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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgctacagtacccgagggcgctcttatctcgcctaatcaagtttagtcacactatgaactgctaatgatttttttggtctcttactgcctgctctgcagGGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGGTGTACTTCAGAAAACACCCGAAGAAGCTGTAGCACATTTCTTTGATGTC

Basic information

species Zea mays
transcript GRMZM2G377609_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G377609_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g43390.2 (Oryza sativa), 3'ss of exon 3
atgctacagtacccgagggcgctcttatctcgcctaatcaagttt---agtca-cactatgaactgctaatgatttttttggtctcttactgcctgctctgcagGGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGGTGTACTTCAGAAAACACCCGAAGAAGCTGTAGCACATTTCTTTGATGTC
|||        |       |  || |  |   || |||  | ||    |  || ||||     ||||||||| || ||       |  |    ||||||||||||||||| ||| |||||||| |||||||||||||||| ||||||||||| ||||| |||   |||||||| |||||||||||||| |||||||||||||||
atggactgaaccttctactcattcattacattccaaatacatttctggaaccagcactggaggctgctaatggttcttca----cccaatcttctgctctgcagGGTTGTCAAATCAGCTGGTCCAAAAGGTCATATACTAAACTTGGGCCATGGTGTTCTTGTAAAAACACCAGAAGAAGCTGTAGCTCATTTCTTTGATGTC
















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|32808628|gb|CD960862.1|CD960862
EST:     CCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAG                         GGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTA
genomic: CCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAGgttagttaag ... tgctctgcagGGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTA
EST: gi|78111204|gb|DV529601.1|DV529601
EST:     CCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAG                         GGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGG
genomic: CCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAGgttagttaag ... tgctctgcagGGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGG
EST: gi|24765753|gb|CA400912.1|CA400912
EST:     CCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAG                         GGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGG
genomic: CCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAGgttagttaag ... tgctctgcagGGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGG
EST: gi|24767427|gb|CA402570.1|CA402570
EST:     CCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAG                         GGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGG
genomic: CCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAGgttagttaag ... tgctctgcagGGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGG
EST: gi|74246191|gb|DT654105.1|DT654105
EST:     CCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAG                         GGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGG
genomic: CCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAGgttagttaag ... tgctctgcagGGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGG
EST: gi|67014894|gb|CO443643.1|CO443643
EST:     CCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAG                         GGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGG
genomic: CCAGCATTTCTGTTCTCACCATTACCAGTACTGACTGATGAAATTCGTAGgttagttaag ... tgctctgcagGGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcacactatgaactgctaatgatttttttggtctcttactgcctgctctgcagGGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGGTGTACTTCAGAAAACACCCGAAGAAGCTGTAGCACATTTCTTTGATGTC
                                           cctgctct  CT-rich tract
                  taatgattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgctacagtacccgagggcgctcttatctcgcctaatcaagtttagtcacactatgaactgctaatgatttttttggtctcttactgcctgctctgcagGGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGGTGTACTTCAGAAAACACCCGAAGAAGCTGTAGCACATTTCTTTGATGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- gctacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaatg