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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgttccgacacattggtttcggctaaaagtttaatcttaaatggtatcaagtactaactgatgcttttggcaacacagCCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCTGAAGCGTCCTCGACAGGGGAGTCTCTTTGCTCATTGCGGTTTGCTGCAA

Basic information

species Zea mays
transcript GRMZM2G436981_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G436981_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os07g01490.1 (Oryza sativa), 3'ss of exon 9
gtattgttccgacac------attggtttcggctaaaa-gtttaatcttaaatggtatcaagtactaactgatgcttttggc----aacacagCCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCTGAAGCGTCCTCGACAGGGGAGTCTCTTTGCTCATTGCGGTTTGCTGCAA
|||   |     |||      |    | || || ||   |||  |  ||   |||    ||    | | ||||  | ||  |     |||||||| || || ||||| |||||||||||||| |||||||||||||||||||| || | ||| || |||||||||||  |||||||  | ||||| || ||| 
gtaaattctaagcactcagctaagaatatctgcaaacttgttctagtttccgtggctataatgtgtgaatgattttgttccccttggacacagCCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCAGAGGTGTCGTCTACAGGGGAGTCAATTTGCTCGCTACGGTTCGCAGCAC

upper sequence: GRMZM2G436981_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os03g64415.1 (Oryza sativa), 3'ss of exon 7
gtattgttccgacac---attggtttcggctaaaagtttaat----cttaaatggtatcaagtactaactgatgcttttggc----aacacagCCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCTGAAGCGTCCTCGACAGGGGAGTCTCTTTGCTCATTGCGGTTTGCTGCAA
|||   |     |||     |        ||  ||  ||  |     ||  |||||   ||    | | ||||  | ||  |     ||| |||| || || ||||| |||||||||||||| |||||||||||||||||||| || | ||| || |||||||||||  |||||||  | ||||| || ||| 
gtaaattctaagcactcagctaagaatatctgcaaacttggtatggtttccatggttataatgtgtgaatgattttgttccccttggacaaagCCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCAGAGGTGTCGTCTACAGGGGAGTCAATTTGCTCGCTACGGTTCGCAGCAC
















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|71437937|gb|DR818987.1|DR818987
EST:     AAGAGGAACACGTTCCATTTCGGAACTCAAAGCTGACATATCTGCTCCAG                         CCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCT
genomic: AAGAGGAACACGTTCCATTTCGGAACTCAAAGCTGACATATCTGCTCCAGgtattgttcc ... ggcaacacagCCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCT
EST: gi|211221459|gb|FL045808.1|FL045808
EST:     AAGAGGAACACGTTCCATTTCGGAACTCAAAGCTGACATATCTGCTCCAG                         CCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCT
genomic: AAGAGGAACACGTTCCATTTCGGAACTCAAAGCTGACATATCTGCTCCAGgtattgttcc ... ggcaacacagCCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCT
EST: gi|33097479|gb|CF057439.1|CF057439
EST:     AAGAGGAACACGTTCCATTTCGGAACTCAAAGCTGACATATCTGCTCCAG                         CCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCT
genomic: AAGAGGAACACGTTCCATTTCGGAACTCAAAGCTGACATATCTGCTCCAGgtattgttcc ... ggcaacacagCCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCT

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), 48 (downstream exon)
Score: 113

CAACAAAAGCTTGTCATGTTTAAGTGATGTCATCTTCTCGATTGCAAAGAAAGAGGAACACGTTCCATTTCGGAACTCAAAGCTGACATATCTGCTCCAGgtattgttcc ... ggcaacacagCCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCTGAAGCGTCCTCGACAGGGGAGTCTCTTTGCTCATTGCGGTTTGCTGCAA


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 11

CAACAAAAGCTTGTCATGTTTAAGTGATGTCATCTTCTCGATTGCAAAGAAAGAGGAACACGTTCCATTTCGGAACTCAAAGCTGACATATCTGCTCCAGgtattgttcc ... ggcaacacagCCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCTGAAGCGTCCTCGACAGGGGAGTCTCTTTGCTCATTGCGGTTTGCTGCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 14

CAACAAAAGCTTGTCATGTTTAAGTGATGTCATCTTCTCGATTGCAAAGAAAGAGGAACACGTTCCATTTCGGAACTCAAAGCTGACATATCTGCTCCAGgtattgttcc ... ggcaacacagCCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCTGAAGCGTCCTCGACAGGGGAGTCTCTTTGCTCATTGCGGTTTGCTGCAA


Block sizes: 46 (upstream exon), 26 (downstream exon)
Score: 3

CAACAAAAGCTTGTCATGTTTAAGTGATGTCATCTTCTCGATTGCAAAGAAAGAGGAACACGTTCCATTTCGGAACTCAAAGCTGACATATCTGCTCCAGgtattgttcc ... ggcaacacagCCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCTGAAGCGTCCTCGACAGGGGAGTCTCTTTGCTCATTGCGGTTTGCTGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaagtttaatcttaaatggtatcaagtactaactgatgcttttggcaacacagCCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCTGAAGCGTCCTCGACAGGGGAGTCTCTTTGCTCATTGCGGTTTGCTGCAA
      tttaatcttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgttccgacacattggtttcggctaaaagtttaatcttaaatggtatcaagtactaactgatgcttttggcaacacagCCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCTGAAGCGTCCTCGACAGGGGAGTCTCTTTGCTCATTGCGGTTTGCTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC