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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttctttcactgtgcattggtttatctgatcagtgtttgacaccttgggcactagtttgactgttgagcatatatatttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTTGGGGAGAAAGAAGCAAAGCTTCTCAAGGAGAAGATTGAAGATGAATACC

Basic information

species Zea mays
transcript GRMZM2G146951_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146951_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g17370.1 (Oryza sativa), 3'ss of exon 2
gtttgttctttcactgtgcattggtttatctgatcagtgtttgacaccttgggcactagtttgactgttgagcatatatatttttttcagTTTGAAATGAGGGAGCCTCAGATG-TGTCAAGTAGTCTGCAAGATATCTGTTGGGGAGAAAGAAGCAAAGCTTCTCAAGGAGAAGATTGAAGATGAATACC
|||||||  |  |  | |      ||| | |||| | |  |||| |  |||| |   || || |   || | | | |||  | ||| |||||||||||||| |||||||| ||| |||||| ||||||||||||| ||||| |||||||||||||||||| |||||||||| |||||||||||||| ||| 
gtttgttactctatcgcgt-----tttctttgattatttcttgatatattggtcctaaggttaatattttaacttctat--tctttccagTTTGAAATGAGAGAGCCTCAAATGCTGTCAAATAGTCTGCAAGATTTCTGTCGGGGAGAAAGAAGCAAAGATTCTCAAGGAAAAGATTGAAGATGAGTAC-
















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|78115833|gb|DV534221.1|DV534221
EST:     ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
EST: gi|149012081|gb|EE042501.2|EE042501
EST:     ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
EST: gi|22491002|gb|BU050925.1|BU050925
EST:     ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
EST: gi|31353915|gb|CD438272.1|CD438272
EST:     ATCTCTGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
EST: gi|149095226|gb|EE180848.2|EE180848
EST:     ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
EST: gi|148999936|gb|EE036993.2|EE036993
EST:     ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
EST: gi|148971253|gb|EE022114.2|EE022114
EST:     ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
EST: gi|149080734|gb|EE169796.2|EE169796
EST:     ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
EST: gi|32796252|gb|CD948488.1|CD948488
EST:     ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
EST: gi|13237179|gb|BG355193.1|BG355193
EST:     ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
EST: gi|91871350|gb|EB401373.1|EB401373
EST:     ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
EST: gi|19437149|gb|BM953559.1|BM953559
EST:     ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
EST: gi|148959757|gb|EC905651.2|EC905651
EST:     ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
EST: gi|149023680|gb|EE045933.2|EE045933
EST:     ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACG                         TTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT
genomic: ATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTT

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), 49 (downstream exon)
Score: 151

CTATTCTCTCCCATTCTGCAAGCCGGATACCATAGTTGACAGTGCAGAAAATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTTGGGGAGAAAGAAGCAAAGCTTCTCAAGGAGAAGATTGAAGATGAATACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

CTATTCTCTCCCATTCTGCAAGCCGGATACCATAGTTGACAGTGCAGAAAATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTTGGGGAGAAAGAAGCAAAGCTTCTCAAGGAGAAGATTGAAGATGAATACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 256

CTATTCTCTCCCATTCTGCAAGCCGGATACCATAGTTGACAGTGCAGAAAATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTTGGGGAGAAAGAAGCAAAGCTTCTCAAGGAGAAGATTGAAGATGAATACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 619

CTATTCTCTCCCATTCTGCAAGCCGGATACCATAGTTGACAGTGCAGAAAATCTCGGTGAAGTTCTTCGTGGAGATCGCATTGAAAACTCTCCCTATACGgtttgttctt ... tttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTTGGGGAGAAAGAAGCAAAGCTTCTCAAGGAGAAGATTGAAGATGAATACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtttgacaccttgggcactagtttgactgttgagcatatatatttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTTGGGGAGAAAGAAGCAAAGCTTCTCAAGGAGAAGATTGAAGATGAATACC
                       gtttgac  putative branch site (score: 619)
                                           tatttttttc  putative PPT
                                      atatatatttttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttctttcactgtgcattggtttatctgatcagtgtttgacaccttgggcactagtttgactgttgagcatatatatttttttcagTTTGAAATGAGGGAGCCTCAGATGTGTCAAGTAGTCTGCAAGATATCTGTTGGGGAGAAAGAAGCAAAGCTTCTCAAGGAGAAGATTGAAGATGAATACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG