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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagttgtttttattctcggtttgggtcaaatactcttttattttcatagggtagctttgtctattagtttagtttccatgcgaaagtctcgagatcttatataggtttcttagctccaagtatttttaatttttatacattctgcatgtttgctttctaaagttttgattttcgtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGCCCTGTGGGTGATTTGTTCAATTATGCTGCTCCTGATGATGACACTTTAT

Basic information

species Zea mays
transcript GRMZM2G092131_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092131_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g28840.1 (Oryza sativa), 3'ss of exon 4
gtatagttgtttttattctcggtttgggtcaaatactcttttattttcatagggtagctttgtctattagtttagtttccatgcgaaagtctcgagatcttatataggtttcttagctccaa---gtatttttaatttttatacattctgcatgtttgctttctaaagttttgattttcgtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGCCCTGTGGGTGATTTGTTCAATTATGCTGCTCCTGATGATGACACTTTAT
                                                                                        | ||| |||  || |||| |||| ||||    ||    | || |  ||||| ||          | |  | ||||| ||||||   ||  |  |  | |||||||||||  | ||||| ||||| ||||||||||| ||||||||  |||| ||| | ||||||||||||||||||||||||||| ||||||||| || ||
---------------------------------------------------------------------------------------tgactcaagaattt-tataagtttgttagtcttaatttctgttctatattttcatggtggaaaggtatgaggtttctgaagtttcttttgaca-acttgaagGTATCTTCAAGAACATTGCATATAGCATGGGATGATGCTGGTTGTCTATGTCCTATTGGTGATTTGTTCAATTATGCTGCTCCTAATGATGACAATTCAT

upper sequence: GRMZM2G092131_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G40730.1 (Glycine max), 3'ss of exon 3
gtatagttgtttttattctcggtttgggtcaaatactcttttattttcatagggtagctttgtctattagtttagtttccatgcgaaagtctcgagatcttatataggtttcttagctccaagtatttttaatttttatacattctgcatgtttgctttctaaagttttgattttcgtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGCCCTGTGGGTGATTTGTTCAATTATGCTGCTCCTGATGATGACACTTTAT-
                                                                |||||  ||| |||| |   ||||   |  | ||   || ||  || | |  || ||| |   || |  ||||||   ||   ||  ||||   | ||||              ||||  || |||||||||  ||  | |||||  | |||||||||||||| || ||||||| ||||||||| ||||| ||||||| ||| ||||   |||   |  | | 
---------------------------------------------------------------gtattacatta-tttcta---gaaa--tttaaaatggcatgtatattacatgccttcaa-tgccttca--ttttatcatttggtcacatttgaactttaaaaa------------atgt--agATATCTTCTCAGACGATGCATATACCGTGGGATGAAGCTGGGTGTTTATGCCTTGTGGGTGACTTGTTTAATTATGATGCACCTGG-AATGGAGCCATCTG

upper sequence: GRMZM2G092131_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G39060.1 (Glycine max), 3'ss of exon 4
gtatagttgtttttattctcggtttgggtcaaatactcttttattttcatagggtagctttgtctattagtttagtttccatgcgaaagtctcgagatcttatataggtttcttagctccaagtatttttaatttttatacattctgcatgtttgctttctaaagttttgattttcgtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGCCCTGTGGGTGATTTGTTCAATTATGCTGCTCCTGATGATGACACTTTAT-
                                                                             | ||||  |     | |     ||||||   ||| |      || |  |    |||    |  || |||     | |  | ||     |||  ||||||  |  |  || ||||||| || ||||| |||||  | |||||||||||||| || ||||||||||||||||| ||||| ||||||| ||| ||||   ||   ||  | | 
-----------------------------------------------------------------------------ttcatgt-attacatggtatatttatatttatttatagttgtcaggggt---aaatcaccactcactctat-catgtagtctc----atttaaattttcaaaattctagATATCTTCCCGGACATTGCATATCCCGTGGGATGAAGCTGGGTGTTTATGCCCTGTGGGTGACTTGTTTAATTATGATGCACCTGG-AATAGAACCATCTG

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|89252045|gb|DY623831.1|DY623831
EST:     TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACG                         GTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
genomic: TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACGgtatagttgt ... gtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
EST: gi|91048511|gb|EB158929.1|EB158929
EST:     TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACG                         GTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
genomic: TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACGgtatagttgt ... gtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
EST: gi|149077854|gb|EE166581.2|EE166581
EST:     TTAAACCTAAGCTTT-GATGTTTAAATCCTGGCTCTGGGCATTTGCAACG                         GTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
genomic: TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACGgtatagttgt ... gtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
EST: gi|101390617|gb|EB817243.1|EB817243
EST:     TTAAACCTAAGCTTTTGATGTTTTAATCCTGGCTCTGGGCATTTGCAACG                         GTATCTTCTCGCACATTACATATTGCATGGGAT
genomic: TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACGgtatagttgt ... gtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGAT
EST: gi|93015506|gb|EB641026.1|EB641026
EST:     TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACG                         GTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
genomic: TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACGgtatagttgt ... gtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
EST: gi|76932735|gb|DV173138.1|DV173138
EST:     TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACG                         GTATCTTCTCGCACATTAC
genomic: TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACGgtatagttgt ... gtatgttaagGTATCTTCTCGCACATTAC
EST: gi|101398534|gb|EB821140.1|EB821140
EST:     TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACG                         GTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
genomic: TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACGgtatagttgt ... gtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
EST: gi|71771111|gb|DR969048.1|DR969048
EST:     TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACG                         GTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
genomic: TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACGgtatagttgt ... gtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
EST: gi|71441696|gb|DR831412.1|DR831412
EST:     TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACG                         GTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
genomic: TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACGgtatagttgt ... gtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
EST: gi|71435233|gb|DR816283.1|DR816283
EST:     TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACG                         GTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC
genomic: TTAAACCTAAGCTTTTGATGTTTAAATCCTGGCTCTGGGCATTTGCAACGgtatagttgt ... gtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttatacattctgcatgtttgctttctaaagttttgattttcgtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGCCCTGTGGGTGATTTGTTCAATTATGCTGCTCCTGATGATGACACTTTAT
                                        ttttcgt  CT-rich tract
                             taaagttttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagttgtttttattctcggtttgggtcaaatactcttttattttcatagggtagctttgtctattagtttagtttccatgcgaaagtctcgagatcttatataggtttcttagctccaagtatttttaatttttatacattctgcatgtttgctttctaaagttttgattttcgtatgttaagGTATCTTCTCGCACATTACATATTGCATGGGATGAAGCTGGTTGCTTATGCCCTGTGGGTGATTTGTTCAATTATGCTGCTCCTGATGATGACACTTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT