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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacaaaaaagatgttctcatgtcatactactattataaagcacaaatgtaattgatgattaggtcatccaaaacaaaaatctaggcttaagttcaatctcctgttgctgtgacctatctttttactcaatatgtggctcgtcatttaataaccaatcttgtcatgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGATACCGACCTTACTGAACGTGTTTTAGTTTACCTCTAGGGAAGGAAACTG

Basic information

species Zea mays
transcript GRMZM2G030902_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030902_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 13
gtaa--gcacaaaaaagatgttct-catgtcatac-tactattataaagcacaaatgtaattgat--gattaggtcatccaaaacaaaaatctaggcttaagttcaatctcctgttgctgtgacctatctttttactcaatatgtggctcgtcatttaataaccaatcttgtc-atgctccagTACGGCTATGGCCCCAGC---AGCGGAAGCAGCAGATCAAGGTCGGATTGGCGATACCGACCTTACTGAACGTGTTTTAGT-TTACCTCTAGGGAAGGAAACTG
||||  ||||||| |   | || | | | | || |  | ||   | |   | || | |||||| |  || ||  |     | |||| |  | |||||||||  |   |    |||   ||| ||| || | | |  | ||| |   ||   |||| ||| ||  || |||||  |||  ||||||||| ||||| | ||||   ||  | || |||||||||||| | |||||||||||||||||||||||| | || | |  | ||||   ||  || |       
gtaagtgcacaaatacattattatgcttatgatgcacagtaggcttatatataagt-taattggtccgagtacatttgtgataacagagctgtaggcttaatgttggttcgttgtgattgtcaccaat-tatctgttgaatctcatgcaaatcatctaacaa--aaacttgttgatgtcccagTACGGTTATGGTCACAGCGGAAGTAGCAGTAGCAGATCAAGGGCTGATTGGCGATACCGACCTTACTGAGCCTGCTGTCTTGTTACTGTTAATGATGTTT----
















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|31664298|gb|CD573023.1|CD573023
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|60400512|gb|DN233319.1|DN233319
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|4837587|gb|AI670677.1|AI670677
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|31405984|gb|CD484716.1|CD484716
EST:     ATGGTTCAATGAGATCTTTTGGCAGATTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|60356069|gb|DN223042.1|DN223042
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|4680979|gb|AI629649.1|AI629649
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|60357001|gb|DN223974.1|DN223974
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|32847446|gb|CD987127.1|CD987127
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTATAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCTA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|110218916|gb|EC900814.1|EC900814
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTTTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|110532935|gb|EE037115.1|EE037115
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTTTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|149096473|gb|EE182215.2|EE182215
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTTTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|211425320|gb|FL461581.1|FL461581
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|37375908|gb|CF624436.1|CF624436
EST:     ATGGTTCAATGAGACCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|71304924|gb|DR788592.1|DR788592
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|33103241|gb|CF063201.1|CF063201
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|60338462|gb|DN205435.1|DN205435
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|211096440|gb|FL454801.1|FL454801
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|32938473|gb|CF043292.1|CF043292
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|33098312|gb|CF058272.1|CF058272
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|211440740|gb|FL468428.1|FL468428
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|8666086|gb|BE186902.1|BE186902
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|60343320|gb|DN210293.1|DN210293
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
EST: gi|32911368|gb|CF016180.1|CF016180
EST:     ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAAT                         TACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA
genomic: ATGGTTCAATGAGATCTTTTGGCAGGTTCTGCGGTGGTCTAGATTATAATgtaagcacaa ... catgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttactcaatatgtggctcgtcatttaataaccaatcttgtcatgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGATACCGACCTTACTGAACGTGTTTTAGTTTACCTCTAGGGAAGGAAACTG
                             taataac  putative branch site (score: 1)
                                       tcttgtc  putative PPT
                          atttaataaccaat  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacaaaaaagatgttctcatgtcatactactattataaagcacaaatgtaattgatgattaggtcatccaaaacaaaaatctaggcttaagttcaatctcctgttgctgtgacctatctttttactcaatatgtggctcgtcatttaataaccaatcttgtcatgctccagTACGGCTATGGCCCCAGCAGCGGAAGCAGCAGATCAAGGTCGGATTGGCGATACCGACCTTACTGAACGTGTTTTAGTTTACCTCTAGGGAAGGAAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA