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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattttctctaggggccattgtaaacgattccttacgccctcaaatcccttcatggtgtgatcctgagtggaagggattgatggaaagctgttggtccagTGATCCAGCGGAGAGACCGTCCTTCACTGATATATCTCAAAGGTTGAGGAAAATGGCCGCTGCAATGAATGTGAAGTGAAGGTTCGGAAGCCATATTTGT

Basic information

species Zea mays
transcript GRMZM2G039106_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039106_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g54510.3 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------------------------------------------cattttctctaggggccattgtaaacgattccttacgccctcaaatcccttcatggtgtgatcctgagtggaagggattgatggaaagctgttggtccagTGATCCAGCGGAGAGACCGTCCTTCACTGATATATCTCAAAGGTTGAGGAAAATGGCCGCTGCAATGAATGTGAAGTGAAGGTTCGGAAGCCATATTTGT
                                                                                         ||||  || ||||| ||| || ||| ||||| |||| ||||| ||||| ||||||||||||||||| |||||   | ||||||||| ||||||| ||||||| ||||| ||                                                                                        
gagggactgcttatatatatccagacgctagtgatgctattgtaattgatcaactattcttgtttgtcactaaagtgatcacttatcatatttattccagGGGGCATCGTGAACAATTCCCTACGTCCTCAGATCCCCTCATGGTGTGATCCTGAATGGAAATCACTGATGGAAAACTGTTGGGCCAGTGAACCAGCAGA----------------------------------------------------------------------------------------

upper sequence: GRMZM2G039106_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G07320.1 (Glycine max), 3'ss of exon 13
---------------------------------cattttctctaggggccattgtaaacgattccttacgccctcaaatcccttcatggtgtg----atcctgagtggaagggattgatggaaagctgttggtccagTGATCCAGCGGAGAGACCGTCCTTCACTGATATATCTCAAAGGTTGAGGAAAATGGCCGCTGCAATGAATGTGAAGTGAAGGTTCGGAAGCCATATTTGT---
                                  | ||| ||| |     || || ||| |     ||   |  |||||| |  |||||||||    ||  |   |  |        ||         ||| |     ||   |  |   | | |    | |      | ||| |||   |||  |  |      |  | |||   |           ||| ||   |      |||   
gtgagaaccaagtaacaaacaaaatgcataaagtaatttgtcttgctaaaat-gtgaacaaaattatatatcaccaaatctcgacatggtgtgcaaaattatatatcaatattcaccattttcgtactttgtttgcagGAGGAATTGTGAACAACACTTTACGTCCTCAAATCCCAAC--TTGGTGTGATCCTGAGTGGAAATCTCTAATGGAAAGTTGTTGGGCTTCTGATCCTGTAGA

upper sequence: GRMZM2G039106_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G01190.1 (Glycine max), 3'ss of exon 10
cattttctctaggggccattgtaaacgattccttacgccctc-aaatcccttcatggtgtgatcctgagtggaagggattgatggaaagctgttggtccagTGATCCAGC-GGAGAGACCGTCCTTCACTGAT-ATATCTCAAAGGTTGAGGAAAATGGCCGCTGCAATG--AATGTGAAGTGAAGGTTCGGAAGCCATATTTGT-------
       |||  ||||     ||   |  |||  | ||  ||  |||    |  |  |  ||     || |  |   ||| ||    | |  |||    | |      || ||||  |  |||    |||  | |  ||   ||  |  |  |   ||    |   | ||  ||| |  | || |   | |   | | | |           
------atctttgggc----atatgtggctccaaatgcgttctgaatattctggtactcagaagaacag-gctatatattaatattca-ccattgtcgtactttgtttgcagGAGGAATTGTCAACAACTCTTTACGTCCTCAAATTCCAACATGGTGTGATCCTGAGTGGAAATCTCTAATGGAAAGTTGTTGGGCTTCTGATCCAGTAGA

upper sequence: GRMZM2G039106_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 8
cattttctctaggggccattgtaaacgattcctt--acgccctcaaatcccttcatggtgtgatcctgagtggaagggattgatggaaagctgttggtccagTGATCCAGCGGAGAGACCGTCCTTCACTGATATATCTCAAAG-GTTGAGGAAAATGGCCGCTGCAATGAATGTGAAGTGAAGGTTCGGAAGCCATATTTGT
   |  ||  |   | | |  | | |  ||   |  |  ||    |||    |   | | || | || ||       ||||||||      | |  | |  | | |  || | | |   ||   | |    | | ||| || || | || |    |  |  |  |  ||  |||  ||||    |  ||   |    |   | 
--gtaactacacctgtcttgcttatcttttgtatgtatacctgtgaatgatatagagttatggtactaagacatgtagattgatg----tttctatgacagGAGGTATAGTGAACAA--CGCATTGCGTCCAAAAATCCCACAGTGGTGTGATCCAGAGTGGAAGGGATTGATGGAAAGTTGCTGGACGTCTGAGCCAACAGA

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|6465660|gb|AW191119.1|AW191119
EST:     GCTTACTGGGGAAGAGCCATACTCTGATATGCGTGCTGCTGAAATTATTG                         TGATCCAGCCGAGAGACCGTCCTTCCCTGATATATCTCAAAGGTTGAGGAA
genomic: GCTTACTGGGGAAGAGCCATACTCTGATATGCGTGCTGCTGAAATTATTGgtaatgtcaa ... gttggtccagTGATCCAGCGGAGAGACCGTCCTTCACTGATATATCTCAAAGGTTGAGGAA
EST: gi|83278980|gb|DV942988.1|DV942988
EST:     GCTTACTGGGGAAGAGCCATATTCTGATATGCGTGCTGCTGAAATTATTG                         TGATCCAGCCGAGAGACCGTCCTTCACTGATATATCTCAAAGGTTGAGGAA
genomic: GCTTACTGGGGAAGAGCCATACTCTGATATGCGTGCTGCTGAAATTATTGgtaatgtcaa ... gttggtccagTGATCCAGCGGAGAGACCGTCCTTCACTGATATATCTCAAAGGTTGAGGAA
EST: gi|83278211|gb|DV942219.1|DV942219
EST:     GCTTACTGGGGAAGAGCCATACTCTGATATGCGTGCTGCTGAAATTATTG                         TGATCCAGCCGAGAGACCGTCCTTCACTGATATATCTCAAAGGTTGAGGAA
genomic: GCTTACTGGGGAAGAGCCATACTCTGATATGCGTGCTGCTGAAATTATTGgtaatgtcaa ... gttggtccagTGATCCAGCGGAGAGACCGTCCTTCACTGATATATCTCAAAGGTTGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccttcatggtgtgatcctgagtggaagggattgatggaaagctgttggtccagTGATCCAGCGGAGAGACCGTCCTTCACTGATATATCTCAAAGGTTGAGGAAAATGGCCGCTGCAATGAATGTGAAGTGAAGGTTCGGAAGCCATATTTGT
                              gattgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattttctctaggggccattgtaaacgattccttacgccctcaaatcccttcatggtgtgatcctgagtggaagggattgatggaaagctgttggtccagTGATCCAGCGGAGAGACCGTCCTTCACTGATATATCTCAAAGGTTGAGGAAAATGGCCGCTGCAATGAATGTGAAGTGAAGGTTCGGAAGCCATATTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attgatg