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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccctctggcctccttttctgtttgatcacatatgcacttgttcccccatggttcttggtttccttcagatctggtgcttgtgtcatcggtttcctcaattgtctggcatctgcattgactcatgatgggtgatgctatgctgtgttctgtggtgtttgtctcag

Basic information

species Zea mays
transcript GRMZM2G154890_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154890_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g22140.1 (Oryza sativa), 5'ss of exon 2
--AATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccctctggcctccttttctgtttgatcacatatgcacttgt-tcccccatggttcttggtttccttcagatctggtgcttgtgtcatcggtttcctcaattgtctggcatctgcattgactcatgatgggtgatgctatgctgtgt-tctgtggtgtttgtctcag
      |  |      || |  |  |  |  ||    |||||||| |||||||| ||||| ||||||||||||||||||||||||||||||||||||||||||||||  ||| |   || ||      ||||     | | |||  || | |   | ||  ||||   |    |   ||||||| ||||| |   |  ||| |            | |  |   |||| |  |  ||  ||||||| |   | |  ||| |||  |    | |||
CGGGGGCGGCGAAGAGTCCCGTGAGCGCCTCCTAG--ATGGGGCTGCTCAGCATCATCCGGAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggtgcccccct-ccacccccagagttt-----cttttgcgattctgtgggcaatccttctctctccattctggatctggcgcttgagcggttcgttcctct---------gtagatttcttgattttttgtgcctgatgctgtctggggaatctatgggttcacccgcag

upper sequence: GRMZM2G154890_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S62_133V6.2 (Physcomitrella patens), 5'ss of exon 1
AATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccctctggcctccttttctgtttgatcacatatgcacttgttcccccatggttcttggtt--tccttcagatctggtgcttgtgtcatcggtttcctcaattgtctggcatctgcattgactcatgatgggtgatgctatgctgtgttctgtggtgtttgtctcag
 | | |   |      |  |        |  |||||||||| | || |  || ||| | ||  | ||||| ||||||||||||||||| ||| |||||||||| |     ||    || || ||     |  | |    ||  | ||||| |   | | |   ||||  |  ||||  ||||||  |  |||| ||   || |||| |||       | |||  ||  |  |||||   || | | |  ||||| |    |            
TAACTCGGATTGAAATTTGCAAGAAGGTATCGATCATGGGGTTGCTGACGATCATCAGGAAAGTGAAGCGGAAGGAGAAGGAGATGCGGATCTTCATGGTgtatgtg--ttcaactctgctgtttcagcttgtgatcggtgtccctgttctc---taggttcgggttgataattcatttctggt--tgatgtcttca--tttctcagttg------gtatgctgtgggtt-tgatgta-gacgtt-tcttgtgtgcctcag------------

upper sequence: GRMZM2G154890_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ26161 (Selaginella moellendorffii), 5'ss of exon 1
AATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccctctggcctccttttctgtttgatcacatatgcacttgttcccccatg-gttcttggtttccttcagatctggtgcttgtgtcatcggtttcctcaattgtctggcatctgcattgactcatgatgggtgatgctatgctgtgttctgtggtgtttgtctcag
                                   |||||||| ||||  || ||||||||| | ||||||||||||||||| |||||||| ||||||||||| |||| ||||  |   || |     | ||||     |||  |  |    || || |   ||| |||||  |  |                                                                                               
-----------------------------------ATGGGGCTGCTCACGATCATCCGCAAGGTGAAGCGCAAGGAGAAGGAAATGCGCATTCTCATGGTgtaagctctctct--ctctctctctctctcgatctttcttgcggtgctatgtccttgcgcatttgatttccgccgcag----------------------------------------------------------------------------------------------

upper sequence: GRMZM2G154890_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ10782 (Selaginella moellendorffii), 5'ss of exon 1
AATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccctctggcctccttttctgtttgatcacatatgcacttgttcccccatggttcttggtttccttcagatctggtgcttgtgtcatcggtttcctcaattgtctggcatctgcattgactcatgatgggtgatgctatgctgtgttctgtggtgtttgtctcag
                                   |||||||| ||||  || ||||||||| | ||||||||||||||||| |||||||| ||||||||||| |||| ||||   |||  | ||  | |     |||  |    | |  ||    |  | ||| |||||  |  |                                                                                               
-----------------------------------ATGGGGCTGCTCACGATCATCCGCAAGGTGAAGCGCAAGGAGAAGGAAATGCGCATTCTCATGGTgtaagctctctct---ctctctctcgatct---ttcatgcggtgctatgtccttgcgcat-ttgatttccgccgcag----------------------------------------------------------------------------------------------

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|91874746|gb|EB404703.1|EB404703
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|60337602|gb|DN204575.1|DN204575
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCAGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|78112616|gb|DV531010.1|DV531010
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|71318964|gb|DR796231.1|DR796231
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|5932640|gb|AW057001.1|AW057001
EST:     ATCCTCATGGT                         TGGCCTGGACAACTCAGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|78082479|gb|DV510891.1|DV510891
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|211102305|gb|FL158952.1|FL158952
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCAGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|89248462|gb|DY620248.1|DY620248
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|91875540|gb|EB405497.1|EB405497
EST:     TTATCCGCAAGATCAAGCGCAAGGAGAAGGAAATGCGCATCCTCATTGGT                         TGGCCTGTACAACTCGGGGAAAACAACCATCGTTTCTCAAGATCAATGGG
genomic: TTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCAT-GGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTT-CTCAAGATCAATGGG
EST: gi|50335743|gb|CO530869.1|CO530869
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATG-T                         -GGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|76016499|gb|DT943669.1|DT943669
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|211104769|gb|FL158955.1|FL158955
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCAGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|50339681|gb|CO534807.1|CO534807
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|34391377|gb|CF384605.1|CF384605
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|78114767|gb|DV533155.1|DV533155
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|74239326|gb|DT647240.1|DT647240
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|89755818|gb|DY686096.1|DY686096
EST:     TTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCCATCCTCATGGT                         TGGCCTGGACAACTCGGGGAAGACCAACCATCGTTCTCAAGATCAATGGGG
genomic: TTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGC-ATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGAC-AACCATCGTTCTCAAGATCAATGGGG
EST: gi|86469538|gb|DY235908.1|DY235908
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
EST: gi|76286526|gb|DV026094.1|DV026094
EST:     ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGT                         TGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA
genomic: ATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccc ... tttgtctcagTGGCCTGGACAACTCGGGGAAGACAACCATCGTTCTCAAGATCAATGGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATCCTCATGGTgtaggctccctctggcctccttttctgtttgatcacatatgcacttgttcccccatggttcttggtttccttcagatctggtgcttgtgtcatcggtttcctcaattgtctggcatctgcattgactcatgatgggtgatgctatgctgtgttctgtggtgtttgtctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG