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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattagccctttctaaatacttgttatgactttgcagcagctcttttttcccttcagttttcttctttttctaatgccccttctattttcacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTATATTGACAGGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCC

Basic information

species Zea mays
transcript GRMZM2G142553_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142553_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g53630.1 (Oryza sativa), 3'ss of exon 10
-----taattagccc--tttctaaatacttgttatgactttgcagcagctcttttttcccttcagttttcttctttttctaatgccccttctattttcacctgac-agGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTATATTGACAGGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCC
     ||  || ||   ||| ||| ||   ||||| | | ||   |||   |  |     |  | |  |  |  ||  ||      |||||||||||||| |  | |||||||| ||||||||||  ||||||| |||||  ||||||||||| | || ||||| |||||||||||||| || ||||||||| |||||| ||||  ||
actactatatatccagatttataactaaaagttat-attctgggacagaggtggtggttttctaatggt--tgcttggctg-----ccttctattttcacatatccagGTGCCAAGTCAGCGTAATAAGTATGACTGTGGTATCTTTATGCTTCATTACATTGAGAGGTTTATTCAAGAGGCACCAGAGAGGCTGACAAGAGAGAACC
















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|149000476|gb|EE037652.2|EE037652
EST:     GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAG                         GTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
genomic: GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
EST: gi|32945884|gb|CF050703.1|CF050703
EST:     GGAGGATATGGAGGCGTCTTTCAAAAAATATCAATAGGGAAAAGATTGAG                         GTGCCACGTCAGGGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
genomic: GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
EST: gi|193502411|gb|AM939258.1|AM939258
EST:     GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAG                         GTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
genomic: GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
EST: gi|93014963|gb|EB640483.1|EB640483
EST:     GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAG                         GTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
genomic: GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
EST: gi|71305064|gb|DR788669.1|DR788669
EST:     GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAG                         GTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
genomic: GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
EST: gi|193502468|gb|AM939287.1|AM939287
EST:     GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAG                         GTGCCACGTCAGCGTAACGAGTATAATTGTGGCCTCTTTATGCTTTACTAT
genomic: GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
EST: gi|86471376|gb|DY237746.1|DY237746
EST:     GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAG                         GTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
genomic: GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
EST: gi|148992843|gb|EE033670.2|EE033670
EST:     GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAG                         GTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
genomic: GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
EST: gi|149000422|gb|EE037593.2|EE037593
EST:     GGAGGATAGGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAG                         GTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
genomic: GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
EST: gi|71767171|gb|DR965108.1|DR965108
EST:     GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAG                         GTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT
genomic: GGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTAT

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: 49 (upstream exon), 46 (downstream exon)
Score: 74

AGAACGGTGGCACCTAGGGATGGATTCGTCTTATGATATTCCATTTTCAGGGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTATATTGACAGGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 95

AGAACGGTGGCACCTAGGGATGGATTCGTCTTATGATATTCCATTTTCAGGGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTATATTGACAGGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 123

AGAACGGTGGCACCTAGGGATGGATTCGTCTTATGATATTCCATTTTCAGGGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTATATTGACAGGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 77

AGAACGGTGGCACCTAGGGATGGATTCGTCTTATGATATTCCATTTTCAGGGAGGATATGGAGGCGTCTTTCGAAAAATATCAATAGGGAAAAGATTGAGgtaagaggcc ... cacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTATATTGACAGGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcccttcagttttcttctttttctaatgccccttctattttcacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTATATTGACAGGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCC
                        ttctaat  putative branch site (score: 77)
             ttttcttctttttcta  CT-rich tract
                     tttttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taattagccctttctaaatacttgttatgactttgcagcagctcttttttcccttcagttttcttctttttctaatgccccttctattttcacctgacagGTGCCACGTCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTATATTGACAGGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - gcagcag