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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagagagggattgtgcagcattgtttatggcacttgagtggagtgcctttctgaccaggggtttctttgctttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTTTGCATCCTTCAATGAGGAGTTGTTCAAGGAGATCACACAGCTTCTAACC

Basic information

species Zea mays
transcript GRMZM2G030422_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030422_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 2
gtaagta-gagagggattgtgcagcattg----tttatggcacttgagtggagtgcctttctgaccaggggtttctttgctttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTTTGCATCCTTCAATGAGGAGTTGTTCAAGGAGATCACACAGCTTCTAACC
||||||| | ||||||   ||   |        |||  ||  || |||||||  || || || ||   |||||| ||||||    |  |||||||||||| || ||||| ||||||||||||||||||||||| |||||||| || ||||| || ||||||||||| |||||||||||||||||| | || 
gtaagtatgggagggaacatgtccctacaggaattttaggtgctggagtggaaagcgttgctaact--gggtttgtttgctgctctg-cagGCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTTCGCGTCCTTTAACGAGGAGTTGTTTAAGGAGATCACACAGCTTTTGACG

upper sequence: GRMZM2G030422_T04 (Zea mays), 3'ss of exon 4
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 2
-----------------------gtaagtagagagggattgtgcagcattgtttatggca---cttgagtggagtgcct-ttctgaccaggggtttctttgctttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTTTGCATCCTTCAATGAGGAGTTGTTCAAGGAGATCACACAGCTTCTAACC
                            |         || ||     ||| || |  |    || | |||| | |||  ||||||  |||||   || ||  ||  |  |||||| ||| |  | | ||| || || ||  | ||||||||||| || || ||||| |||||||| || ||  ||| ||||||||| ||||||||||| || 
gtgagtgacaagttttctctttctctctttctctctttttatgttttcttgcttctctcttatctcgtgtggtgagccagttctgataagggggg-ctctgtgttgtttgcagGCAAGATAGAGCGAGGGCAGTGGAGATACTAGTCAAGGACCTCAAAGTGTTTGCGTCCTTCAACGAAGATCTGTACAAGGAGATTACACAGCTTCTTACG

upper sequence: GRMZM2G030422_T04 (Zea mays), 3'ss of exon 4
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtagagagggattgtgcagcattgtttatggcacttgagtggagtgcctttctgaccaggggtttctttgctttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTTTGCATCCTTCAATGAGGAGTTGTTCAAGGAGATCACACAGCTTCTAACC
        |  | | ||||     |||| ||  |   |||   |||  |  ||  | |    |   || | |  || |    ||||||| ||  |  | || || ||||| ||  | ||||||||||| ||||| ||||| || ||||||||||| || | ||| ||||| ||||||||||| || 
------gtaaggagtttgtttgctattgatt-cgtttcttcgctgg--tagctaacgggtttg---ttacctctctctggcgtcagGCAAGACAGAGCGAAAGCCGTTGAGATTCTCGTCAAGGACCTCAAGGTGTTTGCGTCGTTCAATGAGGACTTATACAAAGAGATTACACAGCTTCTTACT

upper sequence: GRMZM2G030422_T04 (Zea mays), 3'ss of exon 4
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtagagagggattgtgcagcattgtttatggcacttgagtggagtgcctttctgaccaggggtttctttgctttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTTTGCATCCTTCAATGAGGAGTTGTTCAAGGAGATCACACAGCTTCTAACC
        |  | | ||||   | |||| ||  |   |||   ||   |  ||  | |    |     ||| | || |    ||||||| ||  |  | || || ||||| ||  | ||||||||||| ||||| ||||| || ||||||||||| || | ||| ||||| ||||||||||| || 
------gtaaggagtttgtttggtattgatt-cgtttcttcgctga--tatctaacgggtttgttacctctct-ctctggcgtcagGCAAGAAAGAGCGAAAGCCGTTGAGATTCTCGTCAAGGACCTCAAGGTGTTTGCGTCATTCAATGAGGACTTATACAAAGAGATTACACAGCTTCTTACT

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|19058337|gb|BM737004.1|BM737004
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|76288699|gb|DV028267.1|DV028267
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|18655046|gb|BM499851.1|BM499851
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTGGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCT
EST: gi|18662061|gb|BM501725.1|BM501725
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|22490728|gb|BU050651.1|BU050651
EST:     GGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: GGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|71766923|gb|DR964860.1|DR964860
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|18662063|gb|BM501726.1|BM501726
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|32928255|gb|CF033067.1|CF033067
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|18655047|gb|BM499852.1|BM499852
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggcacttgagtggagtgcctttctgaccaggggtttctttgctttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTTTGCATCCTTCAATGAGGAGTTGTTCAAGGAGATCACACAGCTTCTAACC
                      ttctgac  putative branch site (score: 2)
                                   tttctttgctttcat  putative PPT
                                            tttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagagagggattgtgcagcattgtttatggcacttgagtggagtgcctttctgaccaggggtttctttgctttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTTTGCATCCTTCAATGAGGAGTTGTTCAAGGAGATCACACAGCTTCTAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA