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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctaactccctttaatctattaatgttacaactatatattgcaacttcgccaatttccttgctatggtttgatttgctctctgaaatgtggcagagtgcacgtcttatgtttttgttgttaggttagttctcagaggaactagttccgtgtcttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAATACGATGGCTACAAGGATGACCCTACAGTGCCAGATGACTCGAATACCC

Basic information

species Zea mays
transcript GRMZM2G130230_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130230_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 9
gtctaactccctttaatctattaatgttacaactatatattgcaacttcgccaatttccttgctatggtttgatttgctctctgaaatgtggcagagtgcacgtcttatgtttttgtt-gttaggttagttctcagaggaactagttccgtgtcttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAATACGATGGCTACAAGGATGACCCTACAGTGCCAGATGACTCGAATACCC
                           |||   ||  | |  | | |      || ||  | ||||  |     ||||      ||   |   | | |    || ||||||||| ||  |||   ||||| || |    ||| |||||| |||  ||||| ||||||||||| || ||||||||||| |||| ||| ||||| |||||||| |||||||| || |||||||||||||||||||||||||||||||| || ||||
--------------------------gtact-ttacctttctctattctctacatgtcaatactatattgcagcttgcc-----aatactataatactaagagtattatgttttagtccgtttctttagtactaaataaaaccagttccctgt--taatgccagGTTCTGCAGTCCGTGAACCCTATAAAGCATGATGAGGTTGTCCTTGGACAATACGAGGGGTACAAGGATGACCCTACAGTGCCAGATGACTCAAACACCC
















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|211002848|gb|FL384087.1|FL384087
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
EST: gi|211483716|gb|FL115161.1|FL115161
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTATGCCTGAAGAGGTAGTCCTTGGGCAA
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
EST: gi|67037531|gb|CO464345.1|CO464345
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
EST: gi|6194863|gb|AW146967.1|AW146967
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
EST: gi|211483712|gb|FL115157.1|FL115157
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTATGCCTGAAGAGGTAGTCCTTGGGCAA
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
EST: gi|211483710|gb|FL115155.1|FL115155
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTATGCCTGAAGAGGTAGTCCTTGGGCAA
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
EST: gi|605736|gb|T27548.1|T27548
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTT
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTT
EST: gi|211483711|gb|FL115156.1|FL115156
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTATGCCTGAAGAGGTAGTCCTTGGGCAA
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
EST: gi|211428715|gb|FL387534.1|FL387534
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGAYGAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGYAGTCCTTGGGCAA
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
EST: gi|211483713|gb|FL115158.1|FL115158
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTATGCCTGAAGAGGTAGTCCTTGGGCAA
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
EST: gi|211483714|gb|FL115159.1|FL115159
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTATGCCTGAAGAGGTAGTCCTTGGGCAA
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
EST: gi|37424885|gb|CF650176.1|CF650176
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
EST: gi|33103286|gb|CF063246.1|CF063246
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
EST: gi|18660007|gb|BM500637.1|BM500637
EST:     GAGAAAGTCAAG                         GTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
genomic: GAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA
EST: gi|113701618|gb|EE679122.1|EE679122
EST:     AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAG                         GTTTTGCAATCTGTGAACCCTATTATGCCTGAAGAGGTAGTCCTTGGGCAA
genomic: AAAAGCCTGTCTCCCTTAAGCCTGAGCACATCAGAGATGAGAAAGTCAAGgtctaactcc ... ttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttgttgttaggttagttctcagaggaactagttccgtgtcttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAATACGATGGCTACAAGGATGACCCTACAGTGCCAGATGACTCGAATACCC
                                           tcttaat  putative branch site (score: 3)
                                           tcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctaactccctttaatctattaatgttacaactatatattgcaacttcgccaatttccttgctatggtttgatttgctctctgaaatgtggcagagtgcacgtcttatgtttttgttgttaggttagttctcagaggaactagttccgtgtcttaatgtcagGTTCTGCAATCTGTGAACCCTATTAAGCCTGAAGAGGTAGTCCTTGGGCAATACGATGGCTACAAGGATGACCCTACAGTGCCAGATGACTCGAATACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG