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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgtatctcgttcacattacgtgccggtgcacaaactgagtcgagcctggaaaacattttaccatgacttctgtgacattgctgcatgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAAGTAGTGGCAGAAAAGGAAGGTGTAGCGAGTGGGTACCGTGTTGTCATCA

Basic information

species Zea mays
transcript GRMZM2G143767_T01
intron # 4
splice site 3'
intron type U2

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|6536550|gb|AW224863.1|AW224863
EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
EST: gi|60340294|gb|DN207267.1|DN207267
EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
EST: gi|211478458|gb|FL136947.1|FL136947
EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGANCCAAGGCATACAGAAATCCTGGGCCGGCTTCTTTACGCAGCGAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAA
EST: gi|211478445|gb|FL136934.1|FL136934
EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
EST: gi|211478451|gb|FL136940.1|FL136940
EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
EST: gi|211478456|gb|FL136945.1|FL136945
EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTTCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
EST: gi|211478447|gb|FL136936.1|FL136936
EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCCAAG-CATACAGAAATCCCTGG-CCGGCTCCTTTACGCAGCGA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCC-AAGGCATACAGAAATCC-TGGGCCGGCTCCTTTACGCAGCGA
EST: gi|211478453|gb|FL136942.1|FL136942
EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
EST: gi|211376140|gb|FL136932.1|FL136932
EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAA
EST: gi|211478444|gb|FL136933.1|FL136933
EST:     ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAG                         GCTGAGCCAAGGCATACANGAAATCCTGGGCCGGCTTCTTTACGCAGC
genomic: ACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACA-GAAATCCTGGGCCGGCTCCTTTACGCAGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 61

AGATGAAAATGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAAGTAGTGGCAGAAAAGGAAGGTGTAGCGAGTGGGTACCGTGTTGTCATCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 79

AGATGAAAATGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAAGTAGTGGCAGAAAAGGAAGGTGTAGCGAGTGGGTACCGTGTTGTCATCA


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 30

AGATGAAAATGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAAGTAGTGGCAGAAAAGGAAGGTGTAGCGAGTGGGTACCGTGTTGTCATCA


Block sizes: 45 (upstream exon), 43 (downstream exon)
Score: 47

AGATGAAAATGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgtatct ... atgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAAGTAGTGGCAGAAAAGGAAGGTGTAGCGAGTGGGTACCGTGTTGTCATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgagcctggaaaacattttaccatgacttctgtgacattgctgcatgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAAGTAGTGGCAGAAAAGGAAGGTGTAGCGAGTGGGTACCGTGTTGTCATCA
                                              tgttctt  CT-rich tract
          aaaacatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgtatctcgttcacattacgtgccggtgcacaaactgagtcgagcctggaaaacattttaccatgacttctgtgacattgctgcatgttcttagGCTGAGCCAAGGCATACAGAAATCCTGGGCCGGCTCCTTTACGCAGCGAAAGTAGTGGCAGAAAAGGAAGGTGTAGCGAGTGGGTACCGTGTTGTCATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA