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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggccgacgaagcacctgatcaaaccaactcaacctctcatcaaagtatctctgaaattcccggctaatacagttggttctctcttgatctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGCGGCCTAACTCAGCTCGTCGCCATGCGGTATGGGACCATCCCGATTGTCC

Basic information

species Zea mays
transcript GRMZM2G141399_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141399_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os08g09230.1 (Oryza sativa), 3'ss of exon 13
----------------------gtgggccgacgaagcacctgatcaaa-ccaactcaacctctcatcaaagta-tctctgaaattcccggctaatacagttggttctctcttgatctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGCGGCCTAACTCAGCTCGTCGCCATGCGGTATGGGACCATCCCGATTGTCC
                        | |||       |||||| |||   ||||          ||||||| |  |||   ||| |    |||     | |   |||  |  |  |||||| |||||||| ||||||||||||||||| || || ||||| || ||||| ||||||||  | ||||| || || |||||||| |||||  ||||||| ||||| |
gttagactatgtttaacttatgacgagcctctctcacacctggtcagttccaatatcctacaccatcaaattggtctaaaaaaattgttgctggc-taataatttcagtgat--tctgctacagATATATGCTGGCTCTGACTTCATCCTTGTTCCATCCATCTTTGAACCTTGCGGTTTGACTCAACTTGTTGCCATGCGCTATGGATCCATCCCTATTGTTC
















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|67021517|gb|CO450266.1|CO450266
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|31352858|gb|CD437215.1|CD437215
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|32835013|gb|CD974691.1|CD974691
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|13149461|gb|BG319783.1|BG319783
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGA-CCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|32833105|gb|CD972783.1|CD972783
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|67014870|gb|CO443619.1|CO443619
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|24764332|gb|CA399497.1|CA399497
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|31351712|gb|CD436069.1|CD436069
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGC
EST: gi|24769423|gb|CA404552.1|CA404552
EST:     ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTG                         ATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTG
genomic: ATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTG

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: 36 (upstream exon), 46 (downstream exon)
Score: 41

AATCCAAGCTGATTTTGTCAACCTGGCGAATAAGCTCCACGGCGTAAACCATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGCGGCCTAACTCAGCTCGTCGCCATGCGGTATGGGACCATCCCGATTGTCC


Block sizes: 48 (upstream exon), 18 (downstream exon)
Score: 4

AATCCAAGCTGATTTTGTCAACCTGGCGAATAAGCTCCACGGCGTAAACCATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGCGGCCTAACTCAGCTCGTCGCCATGCGGTATGGGACCATCCCGATTGTCC


Block sizes: 36 (upstream exon), 45 (downstream exon)
Score: 4

AATCCAAGCTGATTTTGTCAACCTGGCGAATAAGCTCCACGGCGTAAACCATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGCGGCCTAACTCAGCTCGTCGCCATGCGGTATGGGACCATCCCGATTGTCC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 40

AATCCAAGCTGATTTTGTCAACCTGGCGAATAAGCTCCACGGCGTAAACCATGGGCAAGTGAGGCTTTCCTTGACCTACGACGAGCCTCTCTCGCATCTGgtgggccgac ... tctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGCGGCCTAACTCAGCTCGTCGCCATGCGGTATGGGACCATCCCGATTGTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtatctctgaaattcccggctaatacagttggttctctcttgatctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGCGGCCTAACTCAGCTCGTCGCCATGCGGTATGGGACCATCCCGATTGTCC
                                  ttctctcttgatct  CT-rich tract
         tgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggccgacgaagcacctgatcaaaccaactcaacctctcatcaaagtatctctgaaattcccggctaatacagttggttctctcttgatctgctgcagATATACGCTGGCTCTGACTTCATTCTGGTCCCATCTATATTTGAGCCTTGCGGCCTAACTCAGCTCGTCGCCATGCGGTATGGGACCATCCCGATTGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC