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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgggatactttgttatgtttggacagttctatgattgggaactgtacagaatgtgacagcatttcttattttaatgtgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTT

Basic information

species Zea mays
transcript GRMZM2G077233_T05
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077233_T06 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g18630.1 (Oryza sativa), 3'ss of exon 9
gttgggatactttgttatgtttggacagttctatgattgggaactgtacagaatgtgacagcat----ttcttattttaatgtgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTT
||  | |    |  ||| ||       | | | |         || | | || ||  | |||||    |||  ||   ||| | |   | ||||||| ||||||||||| |||||||||||||| ||  | || || ||| || |||||||||| ||||| || ||| |||||||||||||||||||||| |
gtaagtagtgatcattacgtcct--ttgctatgtcgcaccagcctttcctgattgcaa-agcataacattccaatcccaatttac--cgaagCTCTGCGAGCGTCTCCCAAGCCCCAATGGCGAATCGGCAGTCGACTGCGATGAGATCTCAAACATGCCGAACCTTTCATTCACCATAGCAAACAAGACCT
















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|78179647|gb|DV550020.1|DV550020
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|32840610|gb|CD980291.1|CD980291
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|12047192|gb|BF729331.1|BF729331
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|76289739|gb|DV029307.1|DV029307
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|116822883|gb|EC866344.1|EC866344
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|76291014|gb|DV030582.1|DV030582
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|32839672|gb|CD979353.1|CD979353
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGA-CGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|60348336|gb|DN215309.1|DN215309
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|60396697|gb|DN229564.1|DN229564
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|8577168|gb|BE129805.1|BE129805
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|211384116|gb|FL248479.1|FL248479
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|60346328|gb|DN213301.1|DN213301
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|91876412|gb|EB406369.1|EB406369
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|83278626|gb|DV942634.1|DV942634
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|5915565|gb|AW053206.1|AW053206
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTACGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
EST: gi|6194440|gb|AW146544.1|AW146544
EST:     GCTCCGTGAAAACAAGACAANAAGAACTCATTTTGAATTACGCTAATCAG                         CTCTGTGAGCGT
genomic: GCTCCGTGAAAACAAGACAA-AAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGT
EST: gi|32858947|gb|CD998628.1|CD998628
EST:     AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAG                         CTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT
genomic: AGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCAT

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), 47 (downstream exon)
Score: 386

TGATCTTTTCTGTACTGCTTGTGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 457

TGATCTTTTCTGTACTGCTTGTGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 669

TGATCTTTTCTGTACTGCTTGTGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 605

TGATCTTTTCTGTACTGCTTGTGAGATGGCTGTTGTCTGGATACAGAATCAGCTCCGTGAAAACAAGACAAAAGAACTCATTTTGAATTATGCTAATCAGgttgggatac ... tgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattgggaactgtacagaatgtgacagcatttcttattttaatgtgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTT
                                     ttttaat  putative branch site (score: 605)
                             atttcttattttaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgggatactttgttatgtttggacagttctatgattgggaactgtacagaatgtgacagcatttcttattttaatgtgcattgcagCTCTGTGAGCGTCTCCCTAGCCCCAATGGCGAGTCAACTGTTGATTGCCATCAGATCTCAAAGATGCCAAATCTTGCATTCACCATAGCAAACAAGACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG