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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatctctctccactaacacttgtgtttggaatctctatccaacattttctaatattgcattgtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA

Basic information

species Zea mays
transcript GRMZM2G107639_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107639_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g08270.1 (Oryza sativa), 3'ss of exon 7
-------------gtcatct-ctctccactaacacttgtgtttggaatctctatccaacattttctaatattgcattgtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA
              ||||   |  | |||  |||||||  || |   |  || |  |  ||||  ||||||||||   |  |||||||| |||||||| ||||||| ||||||||||||||||||||| |||||||||||||||||
gtaacctgtctctctcattcacagttcacgcacacttgcattcgaggtgact-ttaattatttcttaatattgcaccattgttccagAGAATTTCAGAACTGTGCAGAAATGCTGGTGCATGGCTTGTAGTTGACAATACCTATGA

upper sequence: GRMZM2G107639_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g08270.4 (Oryza sativa), 3'ss of exon 7
-------------gtcatct-ctctccactaacacttgtgtttggaatctctatccaacattttctaatattgcattgtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA-----------------------------------------
              ||||   |  | |||  |||||||  || |   |  || |  |  ||||  ||||||||||   |  |||||||| |||||||| ||||||| ||||||||||||||||||||| |||||||||||||||||                                         
gtaacctgtctctctcattcacagttcacgcacacttgcattcgaggtgact-ttaattatttcttaatattgcaccattgttccagAGAATTTCAGAACTGTGCAGAAATGCTGGTGCATGGCTTGTAGTTGACAATACCTATGAGTAAGTTAGTACTCAATTACTGATTATTGCTCAACTGCAAC

upper sequence: GRMZM2G107639_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G01520.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------------------------------------------------------------------------gtcatctctctccactaacacttgt-gtttggaatctctatccaacattttctaatattgcattgtcatt--ccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA
                                                                                                                        |||  || |  | ||||  || | |||   ||  | | |  || ||||   | ||||   |  |  ||   ||||||||||||||||| ||||| ||||||||  | |||||||| ||||| ||||| || ||
gtctctctctctcactctccctctgaatttatcaacagctagtacgattttagaagtgatccttttttaatcttcttgtgtggccaccagataatattccccaagaatatgctgattgaccataactgtaaagtaactttttttgttataaaaatatttataaaatttctgagtattttctcttatttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAATACATACGA

upper sequence: GRMZM2G107639_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G43830.3 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------------------------------------------------------gtcatctctctc--cactaacacttgtgtttggaatctctatccaacattttctaatatt-----gcattgtcattc-------cagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA
                                                                                                                 |   |  |  |   |  |  | || | |||    | | |||  || |  || ||| |||     | ||| ||  |        ||||||||||||||||| ||||| ||||||||  | |||||||| ||||| ||||| || ||
gtctctctctctctctctttctctctctctctcccactgaaattatcaacagctagtatgattttagaacttcttgggtggccaccagataatattcccaaagaatatgctgattgaccataacagtagcagtagtttttttttttttttttataaaaaaaattataaaatttctgagtattttctcttatttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAATACATACGA

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|148932368|gb|EC876010.2|EC876010
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|67030337|gb|CO459086.1|CO459086
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACNAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|148947797|gb|EC893285.2|EC893285
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|148963140|gb|EE014107.2|EE014107
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|149112179|gb|EE295100.2|EE295100
EST:     GAATCCGGGGAACCCCTCTGGAGCTTTTATTCTCA-GGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: GAATCCGGGGAACCCCTCTGGAGCTTTTATTC-CAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|149037081|gb|EE155270.2|EE155270
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|149084340|gb|EE173781.2|EE173781
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGGTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|76286951|gb|DV026519.1|DV026519
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTTGACA-
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTT-GACAA
EST: gi|50325408|gb|CO520534.1|CO520534
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
EST: gi|67011573|gb|CO440322.1|CO440322
EST:     TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAG                         AGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT
genomic: TGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAAT

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: 275

GGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCACTGTTGTGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 487

GGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCACTGTTGTGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 291

GGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCACTGTTGTGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1735

GGAGAAGGTTCTGAAAGAAAATGAGCCTATCCCTAAACTTGTCACTGTTGTGAATCCGGGGAACCCCTCTGGAGCTTTTATTCCAAGGCCTATGCTTGAGgtcatctctc ... gtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttgtgtttggaatctctatccaacattttctaatattgcattgtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA
                              ttctaat  putative branch site (score: 1735)
                                              tcattcc  putative PPT
                        aacattttctaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatctctctccactaacacttgtgtttggaatctctatccaacattttctaatattgcattgtcattccagAGGATTTCAGATCTGTGCAAAAATGCTGGTGCATGGCTTGTGGTTGACAATACCTATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG