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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtagtagtagcctcttctgccttgtagtgctgctattggaatttttattaatgtctcatttttttaatctgtcacttcactgttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC

Basic information

species Zea mays
transcript GRMZM2G146472_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146472_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g06760.1 (Oryza sativa), 3'ss of exon 3
gttggtagtagtagcctcttctgccttgtagtg-ctgctattggaatttttattaatgtctcatttttttaatctgtcacttcactgttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC
||| ||  ||     | ||||  ||| ||| |  ||  ||    | || || ||         |||||| ||  |    ||  | | || || ||||||||| | || |||||||||||||  ||  ||||||||||  |||| ||||| ||||| |||||||||||||||||||||||||||||
gttagtgctaagtatcacttccacctagtaatatctaataccaaagttattctt-------tgttttttcaacttact-ctaaattttttgttcagAGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC
















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|32830032|gb|CD969710.1|CD969710
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGCTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|28930818|gb|CB334179.1|CB334179
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|32829230|gb|CD968908.1|CD968908
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|15214979|gb|BI431119.1|BI431119
EST:     TGGTTG-TGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: TGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|22542105|gb|BU092543.1|BU092543
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|32841469|gb|CD981150.1|CD981150
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|19822219|gb|BQ048243.1|BQ048243
EST:     TATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTG-TGATATC
genomic: TATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|32839778|gb|CD979459.1|CD979459
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|76930615|gb|DV172453.1|DV172453
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGACATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|24773481|gb|CA408735.1|CA408735
EST:     TTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: TTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|32831818|gb|CD971496.1|CD971496
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|211499004|gb|FL379821.1|FL379821
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTNGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|32828756|gb|CD968434.1|CD968434
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|24774011|gb|CA409265.1|CA409265
EST:     GGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCACGAACACTGCTACTGAATCTGTTGATAT
genomic: GGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCA-GAACACTGCTACTGAATCTGTTGATAT
EST: gi|76918295|gb|DV167234.1|DV167234
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|31356464|gb|CD440821.1|CD440821
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|31359395|gb|CD443752.1|CD443752
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|148933612|gb|EC877493.2|EC877493
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|67031337|gb|CO460086.1|CO460086
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|24961547|gb|CA483556.1|CA483556
EST:     GGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: GGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|31363502|gb|CD447859.1|CD447859
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|31354397|gb|CD438754.1|CD438754
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|24773581|gb|CA408835.1|CA408835
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|29577050|gb|CB617162.1|CB617162
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|149078577|gb|EE167361.2|EE167361
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|148939817|gb|EC884519.2|EC884519
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|32829344|gb|CD969022.1|CD969022
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|60344926|gb|DN211899.1|DN211899
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|32839644|gb|CD979325.1|CD979325
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|32839620|gb|CD979301.1|CD979301
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|148942045|gb|EC887040.2|EC887040
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|31364520|gb|CD448875.1|CD448875
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGGCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|149101884|gb|EE287439.2|EE287439
EST:     CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG                         AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
genomic: CCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATC
EST: gi|32839645|gb|CD979326.1|CD979326
EST:     TAAATAAGACAGTTAT-GTTGTTGAATTG-TCCAAG                         AGAAGGGTTGAAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATAT
genomic: TAAATAAGACAGTTATGGTTGTTGAATTGAT-CAAGgttggtagta ... gttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaatttttattaatgtctcatttttttaatctgtcacttcactgttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC
                                              ttcgtcc  CT-rich tract
     tttttattaatgtctc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtagtagtagcctcttctgccttgtagtgctgctattggaatttttattaatgtctcatttttttaatctgtcacttcactgttcgtccagAGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG