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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttggaagcggctacattcttgcatggttgtcctttgcataaaaaattgttgtaagcaccatatggtcaggttataaaatatcagctctatacttc...

Basic information

species Zea mays
transcript GRMZM2G031107_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031107_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g38840.1 (Oryza sativa), 5'ss of exon 8
ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttggaagcggctacattcttgcatggttgtcctttgcataaaaaat----tgttgtaagcaccatatggtcaggttataaaatatcagctctatacttc
|| ||||| |  ||||||||||| ||||||||||||||||| || ||||||||||||||||| ||||| ||   ||  ||| |||||||   || | ||  |   ||| |    |||||||||||| ||||| |   |       ||||   || || |  | 
ATTGTATTCAGAGAGGACTTTGGGACTGAAGGACGTGGAGGGTACTTTGATCAATATGGgtatgttgggagtaactttatt-ttgcatgaaagttccttttactgaaagtattttgttgtaagcac-atatgcttgtgactgtggatat--actataaaagtg

upper sequence: GRMZM2G031107_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA16G06850.1 (Glycine max), 5'ss of exon 8
ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttggaagcggctacattcttgcatggttgtcctttgcataaaaaattgttgtaagcaccatatggtcag-gttataaaatatcagctctatacttc--------------------------
|| || || |  ||||| ||||||||||| || ||||| ||||||||||| || |||||||| ||    |     |   || | ||   ||| || | ||  | ||    || | |       ||| ||   |  ||| || | |  ||| | |  | |                           
ATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAGTATGGgtatgtgtagaa---ttttgttttagcgaagttctcatctgagtcaaggcatgct-tctctttaatagggaaggtattacaacaaagtagcccaaatcattatttactgtttttctttattttgcag

upper sequence: GRMZM2G031107_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA19G24250.3 (Glycine max), 5'ss of exon 8
ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgt-tggaagc-------ggctacattcttgcatggttgtcctttgcataaaaaattgttgtaagcaccatatggtcaggttataaaatatcagctctatacttc
|| || || |  ||||| ||||||||||| || ||||| ||||||||||| ||||||||||| || | |||          || |  ||||   ||| ||     ||||  || |    ||| |||     ||    | | |||   ||| |  || | |  |    
ATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGGgtatgtgtagaaatttgttttagcgaagttctcagatgattagtgattgc-caatagtaggttctaaa----atgaaatgatgttgagaaaaacaagtttttgaa---

upper sequence: GRMZM2G031107_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 5'ss of exon 8
ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttggaagcggctacattcttgcatggttgtcctttgcataaaaaattgttgtaagcaccatatggtcaggtt--ataaaatatcagctctatacttc----
|| || || | ||| || |||||||||||||| ||||| |||||||||||  ||||||||||       |    ||   |   ||  |  |||| |||   |||     ||  || |     ||   | |||  |   || | || |   ||   | |  |    
ATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGGgta-----atactttctttttgagtgtcttcttgttcttcatatagggtcttaatg-agatgacaccagttcatttctgatgacatcttcacttcttgccacacag

upper sequence: GRMZM2G031107_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 5'ss of exon 8
ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttggaagcggctacattcttgcatggttgtcctttgcataaaa----aattgttgtaagcaccatatggtcaggttataaaatatcagctctatacttc-----
|| || || | |||||| |||||||||||||| ||||| |||||||||||| |||||||||| |           |  |  || ||| ||   ||  |   ||||      | || || | |||| |   |  |||  ||||  ||| |    |  | ||||      
ATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGGgtatgcca-------ttgaacactagcaagggaatcagtaatataaggctttattttttattagcatctctttttca--ttattgaatgtatatttaaaacttattatg

upper sequence: GRMZM2G031107_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S222_130V6.2 (Physcomitrella patens), 5'ss of exon 8
ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgt----tggaagcggctacattcttgcatggttgtcctttgcataaaaaattgttgtaagcaccatatggtcaggttata-aaatatcagctctatacttc
|| || ||||||||||||||||||||| ||||||| || || ||||||||| | |||||||| ||    |  |||  | |   ||||||  | | |    ||   |     | | |||| |   |    |   | ||     | ||| | || |  |  | || 
ATTGTTTTTAAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGGgtaagtgatctaaaaggagttcagttcttgatttgctagattt---acgcgtactggttgcacaaattgga-aatgagtcagcagaaacaccatcatttaattt-

upper sequence: GRMZM2G031107_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S73_244V6.3 (Physcomitrella patens), 5'ss of exon 8
ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttggaagcggctac--attcttgcatggttgtcctttgcataaaaaatt-gttgtaagcaccatatggtcaggttataaaatatcagctctatacttc
|| || || |||||||||||||||||||||||||| || || || || ||  |||| ||||| ||    |     | |   |  |||| |   |   |      ||| | |   |||| | |||  |     ||||   | | |||   |    | ||    
ATTGTTTTCAAGGAGGACTTTGGAACTGAAGGACGAGGCGGCTACTTCGACGAATACGGgtaggtcactaagatttcccggtcattgcttatatacacacacgttaacacaccagttgcacgcag-aggaaatcagtggagagaattaaaatattttaaa--

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|111146774|gb|EE258268.1|EE258268
EST:     AAGGAAGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG                         TATCATTCGTGATATCATTCAAAACCACTTGTTGCAG
genomic: AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
EST: gi|60672339|gb|DN475101.1|DN475101
EST:     AAGGAAGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG                         TATCATTCGTGATATCATTCAAAACCACTTGTTGCAG
genomic: AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
EST: gi|18661166|gb|BM501251.1|BM501251
EST:     NAGGNGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG                         TATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
genomic: AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
EST: gi|76281884|gb|DV021452.1|DV021452
EST:     AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG                         TATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
genomic: AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
EST: gi|78109019|gb|DV527436.1|DV527436
EST:     AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG                         TATCATTCGTGATATCATTCAGAACCACTTGTTGCAG
genomic: AAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttgga ... gttgatgcagTATCATTCGTGATATCATTCAGAACCACTTGTTGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGGgtacgttggaagcggctacattcttgcatggttgtcctttgcataaaaaattgttgtaagcaccatatggtcaggttataaaatatcagctctatacttc

- - - -  AAGGAG
- - - - -  GGAGGA
- - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaaa