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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtgtttctacttgttcaggataattatacaagcggtgaactcaggcccaatttaactccatctaatctgcagGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG

Basic information

species Zea mays
transcript GRMZM2G381051_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381051_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA12G07570.1 (Glycine max), 3'ss of exon 9
-----------------gtatggtgtttctacttgttcaggataattatacaagcggtgaactcaggcccaatttaactccatctaatctgcagGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG
                 ||  |   |||||| || |     ||   ||  ||                |  ||  ||    ||       |||||||||||||||| |||||||| |||||||| |||  ||||||||| || ||  ||||||| ||||
gtatgtatgcatgttctgtgagaaatttctatttataatccattcctaaccactttccctcactttaactgataaaatggaattctgcgggcagGTGTGAGCTTGTCTTTGAGAATTGCTTTGTTCCAGACGAAAATGTTCTTGGGAAAGAAGGGAAAG

upper sequence: GRMZM2G381051_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 9
gtatg-gtgtttctacttgttcaggataattatacaagcggtgaactcaggcccaatttaactccatctaa---------------tctgc----agGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG
|||||  ||  | |  |  |    || | || || |     |  | ||     || |||  |||  | |||               |||||    |||||||||||||| |||||||| |||||||| |||  ||||||| | || ||  ||||||| ||||
gtatgtatgcatatgttc-tgtgagaaatttctatatataatccattcctaatcactttccctcactttaactgacaaaatgggattctgcgggcagGTGTGAGCTTGTCTTTGAGAATTGCTTTGTTCCAGACGAAAATATTCTTGGGAAAGAAGGGAAAG

upper sequence: GRMZM2G381051_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT3G45300.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatggtgtttctacttgttcaggataattatacaagcggtgaactcaggcccaatttaact--------ccatctaatct-------------gcagGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG
    |   |  | | |   ||| |||||  |||   | | | || | |  |||  ||| |||        |  |||||  |             ||||||||||||||||||||||||| ||||| || |||   |||||| | || |   | ||||| ||||
----gtaatccccattctctcaagataaaaatatctgtg-taaattaaatccctttttcactgtctctttctctctaacatctgtctctcctgagcagGTGTGAGCTTGTTTTTGAGAATTGCTTCGTTCCAGAGGAAAATATTCTAGACAAGGAAGGAAAAG

upper sequence: GRMZM2G381051_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv06s0004g03140.t01 (Vitis vinifera), 3'ss of exon 9
---------------gtatggtgtttctacttgttcaggataattatacaagcggtgaactcaggcccaatttaactccatctaatctgcagGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG
                 |   || | |  ||| ||        || |  ||  || ||    | |   | ||| | |  | | ||  ||||||||||||||||| |||||||| |||||||| |||   |||||||| || ||  | ||||| ||||
gtaagcctcattactacagcatgctcccccttttttctctcttttctgaaactggagaggatatgataattttcatt--aacaaaattgcagGTGTGAGCTTGTCTTTGAGAATTGCTTTGTTCCAGAAGAAAATGTTCTTGGGCAGGAAGGGAAAG

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|148952108|gb|EC897900.2|EC897900
EST:     GGCATGAGAGGAAGCGACAC                         GTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGG
genomic: GGCATGAGAGGAAGCGACACgtatggtgtt ... taatctgcagGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGG
EST: gi|148928298|gb|EE284912.2|EE284912
EST:     TTCAGTACTGCTCAGAAGTTGGACAAACTTGGCATGAGAGGAAGCGACAC                         GTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGG
genomic: TTCAGTACTGCTCAGAAGTTGGACAAACTTGGCATGAGAGGAAGCGACACgtatggtgtt ... taatctgcagGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGG
EST: gi|148949902|gb|EC895400.2|EC895400
EST:     GCATGAGAGGAAGCGAACAC                         GTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCG
genomic: GCATGAGAGGAAGCG-ACACgtatggtgtt ... taatctgcagGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCG
EST: gi|31352282|gb|CD436639.1|CD436639
EST:     TTCAGTACTGCTCAGAAGTTGGACAAACTTGGCATGAGAGGAAGCGACAC                         GTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGG
genomic: TTCAGTACTGCTCAGAAGTTGGACAAACTTGGCATGAGAGGAAGCGACACgtatggtgtt ... taatctgcagGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGG
EST: gi|60356707|gb|DN223680.1|DN223680
EST:     AGTACTGCTCAGAAGTTGGACAAACTTGGCATGAGAGGAAGCGACAC                         GTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGG
genomic: AGTACTGCTCAGAAGTTGGACAAACTTGGCATGAGAGGAAGCGACACgtatggtgtt ... taatctgcagGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGG
EST: gi|40333885|gb|CK367955.1|CK367955
EST:     TTCAGTACTGCTCATAAGTTGGACAAACTTGGCATGAGAGGAAGCGACAC                         GTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGG
genomic: TTCAGTACTGCTCAGAAGTTGGACAAACTTGGCATGAGAGGAAGCGACACgtatggtgtt ... taatctgcagGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGG
EST: gi|37394249|gb|CF634396.1|CF634396
EST:     TTCAGTACTGCTCAGAAGTTGGACAAACTTGGCATGAGAGGAAGCGACAC                         GTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGG
genomic: TTCAGTACTGCTCAGAAGTTGGACAAACTTGGCATGAGAGGAAGCGACACgtatggtgtt ... taatctgcagGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggataattatacaagcggtgaactcaggcccaatttaactccatctaatctgcagGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG
                                          atctaat  putative branch site (score: 3)
                                      ctccatct  CT-rich tract
     attatacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtgtttctacttgttcaggataattatacaagcggtgaactcaggcccaatttaactccatctaatctgcagGTGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCATGCGAAAATGTCCTCGGTGAAGAAGGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG