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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaggttctgtgccacgtagattattgtagatgtgtcattgctctcagcaccttcacccagagtgggctaaaatattactaattgctgaatcttaacatttccgaacagAATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACTGCCACTGAGAGGACCCTCTGTTGTATTCTGGAGAATTTCCAAAAGGAGG

Basic information

species Zea mays
transcript GRMZM2G172101_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G172101_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g37837.1 (Oryza sativa), 3'ss of exon 8
gtaaaaggttctgtgccacgtagattattgtagatgtgtcattgctctcagcaccttcacccagagtgggctaaaatattactaattgctgaatcttaacatttccgaacagAATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACTGCCACTGAGAGGACCCTCTGTTGTATTCTGGAGAATTTCCAAAAGGAGG
       ||    |  ||| | |||  | ||||||     | |  ||| |            | |||   ||    |||| | | |   |  || || | |||      |||||||||||||| |||||||| || ||||||||| ||||||| || ||||||||||||||||||||||| || |||||| ||||||| ||||| |||||| 
-------gtatcttttcacttggatgctggtagat---caaattatctta------------aaagtcatctgt--tattgccactgatttgatgttcaaatt-----gcagAATGATGAGCAATCCAAGCAATTCGTTCATATGTTGAACTCAACATTGACTGCCACTGAGAGGACCCTTTGCTGTATTTTGGAGAACTTCCAGAAGGAGA

upper sequence: GRMZM2G172101_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g10190.1 (Oryza sativa), 3'ss of exon 8
gtaaaaggttctgtgccacgtagattattgtagatgtgtcattgctctcagcaccttcacccagagtgggctaaaatattactaattgctgaatcttaacatttccgaacagAATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACTGCCACTGAGAGGACCCTCTGTTGTATTCTGGAGAATTTCCAAAAGGAGG
       ||    |  ||| | |||  | || |||     | |  ||| |  |  |||| |               |||||| |||   | ||| || | |||      |||||||| || || |||||||| |||||||||||| ||||||| || ||||||||||||||||||||||| || |||||| ||||||| ||||| | |||| 
-------gtatcatttcacttggatgctggtggat---caaattatcttaaaa--ttcatctgt------------tattaccaatgatttaatgttcaaatt-----gcagAATGACGAACAATCCAAGCAATTTGTTCATATGTTGAACTCAACATTGACTGCCACTGAGAGGACCCTTTGCTGTATTTTGGAGAACTTCCAGAGGGAGA
















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|12045945|gb|BF728175.1|BF728175
EST:     GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAG                         AATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
genomic: GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAGgtaaaaggtt ... ttccgaacagAATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
EST: gi|71766798|gb|DR964735.1|DR964735
EST:     GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAG                         AATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
genomic: GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAGgtaaaaggtt ... ttccgaacagAATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
EST: gi|31352352|gb|CD436709.1|CD436709
EST:     GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAG                         AATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
genomic: GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAGgtaaaaggtt ... ttccgaacagAATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
EST: gi|78180884|gb|DV551257.1|DV551257
EST:     GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAG                         AATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
genomic: GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAGgtaaaaggtt ... ttccgaacagAATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
EST: gi|71766797|gb|DR964734.1|DR964734
EST:     GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAG                         AATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
genomic: GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAGgtaaaaggtt ... ttccgaacagAATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
EST: gi|78113530|gb|DV531921.1|DV531921
EST:     GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAG                         AATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
genomic: GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAGgtaaaaggtt ... ttccgaacagAATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
EST: gi|60400090|gb|DN232897.1|DN232897
EST:     GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAG                         AATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
genomic: GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAGgtaaaaggtt ... ttccgaacagAATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
EST: gi|32932030|gb|CF036842.1|CF036842
EST:     GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAG                         AATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT
genomic: GCACTGACTTTCAGTCAAGGAGACTTGGAATTGGGTATGGCCAGAAAAAGgtaaaaggtt ... ttccgaacagAATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacccagagtgggctaaaatattactaattgctgaatcttaacatttccgaacagAATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACTGCCACTGAGAGGACCCTCTGTTGTATTCTGGAGAATTTCCAAAAGGAGG
                                          catttcc  CT-rich tract
              taaaatattactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaggttctgtgccacgtagattattgtagatgtgtcattgctctcagcaccttcacccagagtgggctaaaatattactaattgctgaatcttaacatttccgaacagAATGATGAGCAGTCCAAGCAGTTTGTTCATATGCTGAACTCTACCTTGACTGCCACTGAGAGGACCCTCTGTTGTATTCTGGAGAATTTCCAAAAGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG