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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgctcaaattgtgctcgttattagtctgtggctgtgcaactcgtgcttaacaagtttggaacttgttgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG

Basic information

species Zea mays
transcript GRMZM2G015989_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 12
gtttgtgctcaaa---ttgtgct----cgttattagtctgtggctgtgcaactcgtgcttaacaagtttg-gaacttgttgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG
|||||| |||  |   |||| ||        || | | ||    | |||| ||||||  |||| | |||  |||| |||     ||||||| ||||||||||| |||||||||||||| |||||||| ||||||||  | |||||||| ||||||||||||||||| |||||||||||||||
gtttgtactctgacatttgttcttaagtacgatgaatatgcaattctgcagctcgtgtgtaacgaatttttgaacatgtatgatttcagGTCCTTGCCAATGATAACTTCAGGTATGGTTACAATGCCGCTACAGGAAAATATGAGGATTTGATGGCTGCTGGTATTATTGATCCCACCAAG

upper sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------------------gtttgtgctcaaattgtgctcgttattagtctgtggctgtgcaactcgtgc-ttaacaagtttggaactt--gttgacatt------------cagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG
                                                  | ||   |||  || || |     ||| |   ||    |  || | ||   |  |  ||  |||| |||  | |||  ||             ||||  |  ||| ||| ||    |  ||||| |||||||| || || ||  | || ||||| ||||||||||||||||| ||||||||||| || 
gtgtgccgtcagtttagattacattgtttacagaagttaaaaactcattatgtgctgtcagtttatggttacatttatttcctgaagttaaaaattgtttatccatgagcctggatctttagctgatgttatattctttatctagGTGTTGTCCAGTGACAATCCAAAATATGGTTACAATGCTGCAACTGGAAAATACGAGGATTTGATGGCTGCTGGTATAATTGATCCCACGAAA
















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|67024753|gb|CO453502.1|CO453502
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|211490742|gb|FL282858.1|FL282858
EST:     AATTGATTGCAAAAWATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|22491347|gb|BU051270.1|BU051270
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|60396892|gb|DN229711.1|DN229711
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|32867895|gb|CF007577.1|CF007577
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|211490743|gb|FL282859.1|FL282859
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|67018624|gb|CO447373.1|CO447373
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCNGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|4226301|gb|AI396408.1|AI396408
EST:     AATTGATTGCAAANAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|7238275|gb|AW573542.1|AW573542
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|78081966|gb|DV510378.1|DV510378
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTCCAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|116821908|gb|EC865261.1|EC865261
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|32867923|gb|CF007605.1|CF007605
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|24769817|gb|CA404946.1|CA404946
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|37379284|gb|CF626383.1|CF626383
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|16926381|gb|BM079449.1|BM079449
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|31356086|gb|CD440443.1|CD440443
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|67018533|gb|CO447282.1|CO447282
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|67024700|gb|CO453449.1|CO453449
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|29544666|gb|CB605046.1|CB605046
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|67021281|gb|CO450030.1|CO450030
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|32935512|gb|CF040324.1|CF040324
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|9952879|gb|BE639462.1|BE639462
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|26457560|gb|CA829143.1|CA829143
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|211181594|gb|FL462638.1|FL462638
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|211033566|gb|FL449282.1|FL449282
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|67017327|gb|CO446076.1|CO446076
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|21891546|gb|BQ744759.1|BQ744759
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|40335213|gb|CK369283.1|CK369283
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|4834970|gb|AI670196.1|AI670196
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|67011543|gb|CO440292.1|CO440292
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|67022736|gb|CO451485.1|CO451485
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|29945491|gb|CB815666.1|CB815666
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|21987876|gb|BQ779404.1|BQ779404
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|37380525|gb|CF627079.1|CF627079
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
EST: gi|19272604|gb|BM888860.1|BM888860
EST:     AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAG                         GTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG
genomic: AATTGATTGCAAAAAATGCAGGCGTTAATGGCAGTGTGGTTACTGAGAAGgtttgtgctc ... tgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtctgtggctgtgcaactcgtgcttaacaagtttggaacttgttgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG
                                          tgttgac  putative branch site (score: 3)
                         ttaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgctcaaattgtgctcgttattagtctgtggctgtgcaactcgtgcttaacaagtttggaacttgttgacattcagGTTCTTGCCAATGAGAACTTCAGGTATGGGTACAATGCGGCTACAGGGGAGTATGAGGACTTGATGGCTGCTGGTATCATTGATCCCACCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT