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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt...

Basic information

species Zea mays
transcript GRMZM2G472625_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 6
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgct---ttctcttttgaaatattcttatcaaaggcttgtttttctttcctt
|||||||||||||| || || |||||||| ||||||||||| || ||||| || ||||||||||| ||| |   |||| ||  |   |  || ||     ||| ||||||||    |   | | |   ||  ||  ||| |   |||      |      
GTTGATCCTCTCACTCATCAAGTCAAGCTATGTGACTTTGGAAGTGCAAAGGTTCTGgtatgttgatttccac-ccttaagagtaatt--tctcagtggtttgatgtatgctgaaattattctagtggtaggctagtcataatgttgacagcataagtgg

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA04G06760.1 (Glycine max), 5'ss of exon 6
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattct-tatcaa-aggcttgtttttctttcctt
|| |||||||| || ||||| || ||||| ||||||||||| || |||||||| || ||||||||   | |||   |||      |||| | |  |    ||||   |   || |         || || | |||  | |   |  |   ||      |
GTGGATCCTCTTACACACCAAGTGAAGCTATGTGACTTTGGAAGTGCAAAAGTTCTAgtatgttgacctccttattttgctttgatgtacttaatttt--ttgtccaacttttccagcaccattatcttttgtatggacaaagtaataactcaaaatgt

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA13G36570.1 (Glycine max), 5'ss of exon 5
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt-
|||||||| ||||| ||||| |||||||||||||| ||||| || |||||||| ||||||||||| | ||||| |  ||    ||         || ||  | |  ||   | |      || |       ||| ||   | | |  | | | ||   
GTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTGgtatgttggtattcttcctgtgcat-ttcactactttatacatgtatgctaccatgttaacagtggacgtggaatattaatatcatatgctacctaccccg

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA12G33950.1 (Glycine max), 5'ss of exon 6
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt-
|||||||  ||||| ||||| |||||||||||||| ||||| || |||||||| ||||||||||  | ||||| |  ||    ||         || ||  | |  ||   | |      || |       ||| || | | | |  | | | ||   
GTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTGgtatgtttgtattcttccagtgcat-ttcactactttatacatgtatgctaccatgttaacagtggacgtggactattaatgtcatatgctacctacccca

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G12370.1 (Glycine max), 5'ss of exon 6
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacat-ccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt-
||||| ||||| || |||||||| ||| | ||||| ||||| || |||||||| ||||||||||| ||| | |||   |   |     |  ||||  |   || |||| ||| |  || | ||   | |   | |      |    |||| | |  |  
GTTGACCCTCTTACACACCAGGTTAAGATATGTGATTTTGGGAGTGCAAAAGTGCTGgtatgttgattt-cattctcagtacacacacacacacacacttttttttgtgtgcatcatcatatgtg-tgtgtctgtgtgtttcaacattttatcttgtca

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G29200.1 (Glycine max), 5'ss of exon 5
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttcc--ttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt-
||||| ||||| || |||||||| ||| | ||||| ||||| || |||||||| ||||||||||| |||  ||  |  |  |     | |  |    | || |  |  ||||  | |   | ||   | |    ||   |  ||||||    | |  || 
GTTGACCCTCTTACACACCAGGTTAAGATATGTGATTTTGGAAGTGCAAAAGTGCTGgtatgttgatttcattctcagtacacacactttttttgtgtgca-tcatcatatgtgtgcgtgtgtgtg-tttcaacattttat-cttgttacattgtaattt

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA06G43620.1 (Glycine max), 5'ss of exon 4
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttcc--ttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt-
||||| ||||| || |||||||| ||| | ||||| ||||| || |||||||| ||||||||||| |||  ||  |  |  |     | |  |    | || |  |  ||||  | |   | ||   | |    ||   |  ||||||    | |  || 
GTTGACCCTCTTACACACCAGGTTAAGATATGTGATTTTGGAAGTGCAAAAGTGCTGgtatgttgatttcattctcagtacaaacactttttttgtgtgca-tcatcatatgtgtgcgtgtgtgtg-tttcaacattttat-cttgttacattgtaattt

upper sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 5'ss of exon 6
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt------
||||||||||||||||| ||||| ||||| ||||| ||||| || ||||| || |||||| ||    ||     || || |   |  |  |    |    ||| ||  || |   |||| | |    |   | |      ||   | ||  ||  ||      
GTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtg---ttgaagaccatgtgtgctccttcttctttt---ttgatgcgtgttccttcttcttatccctgtctctttctctctctctctttattttttgggctc

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|33095534|gb|CF055528.1|CF055528
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG                         ATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
EST: gi|6695759|gb|AW288837.1|AW288837
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG                         GTTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
EST: gi|13198123|gb|BG354164.1|BG354164
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG                         ATTCCTGGTGAACCGAACAT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACAT
EST: gi|6587591|gb|AW244909.1|AW244909
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG                         ATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGNTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
EST: gi|211467509|gb|FL214418.1|FL214418
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG                         GTTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
EST: gi|6696036|gb|AW289144.1|AW289144
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG                         GTTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
EST: gi|9825069|gb|BE575271.1|BE575271
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG                         GTTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt

- - - - - - - - - - -  CAAGCT