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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctttgatctgttatagttttttttgtcagacttgaaacttttctacaagacttggtatttcactgtttggctttcatcattcagGAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACGGATGACCTAAGACATTACTTTGGCAG

Basic information

species Zea mays
transcript GRMZM2G030902_T02
intron # 10
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 10
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 10
gtaagtctttgatctgttatagttttttttgtcagactt-gaaacttttctacaagacttggtatttcactgtttggctttcatcattcagGAGGG---TACTATGGATCCTCTCAAGCAGTGGGCAA---GAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACGGATGACCTAAGACATTACTTTGGCAG
|||||||||    ||   |   |      | | | ||   | ||||||  ||   |  |   | |||  || |||| ||| |||     ||||||    |||||||||||||| |||| | |||||||    |||||||||||||| || ||||||||||| ||||||||||| |||||||| ||||||||      
gtaagtcttctg-ctacgaagatcacaggtttgacacaaagcaactttgttaactggttaaatgtttt-ctatttgacttacattgactagGAGGAGGATACTATGGATCCTCCCAAGGAATGGGCAACAAAAAGATATTTGTTGGCAGGCTTCCACAAGAGGCAAACACGGAGGACCTAAGGCATTACTT------
















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|60356069|gb|DN223042.1|DN223042
EST:     AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAA                         GAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAAgtaagtcttt ... catcattcagGAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|60357001|gb|DN223974.1|DN223974
EST:     TCATCCTGGATCAGCCTATGGAA                         GAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: TCATCCTGGATCAGCCTATGGAAgtaagtcttt ... catcattcagGAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|110218916|gb|EC900814.1|EC900814
EST:     TGTATGATCATCCTGGATCAGCCTATGGAA                         GAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: TGTATGATCATCCTGGATCAGCCTATGGAAgtaagtcttt ... catcattcagGAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|149096473|gb|EE182215.2|EE182215
EST:     AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAA                         GAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAAgtaagtcttt ... catcattcagGAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|37375908|gb|CF624436.1|CF624436
EST:     CAGCTTATGGAA                         GAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: CAGCCTATGGAAgtaagtcttt ... catcattcagGAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|71304924|gb|DR788592.1|DR788592
EST:     TGGATCAGCCTATGGAA                         GAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: TGGATCAGCCTATGGAAgtaagtcttt ... catcattcagGAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|21432115|gb|BQ547605.1|BQ547605
EST:     AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAA                         GAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTT
genomic: AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAAgtaagtcttt ... catcattcagGAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTT
EST: gi|33098312|gb|CF058272.1|CF058272
EST:     AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAA                         GAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAAgtaagtcttt ... catcattcagGAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|32847027|gb|CD986708.1|CD986708
EST:     AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAA                         GAGGGTATTATGGACCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAAgtaagtcttt ... catcattcagGAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|60343320|gb|DN210293.1|DN210293
EST:     AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAA                         GAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
genomic: AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAAgtaagtcttt ... catcattcagGAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTA
EST: gi|26558086|gb|CA830321.1|CA830321
EST:     AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAA                         GAGGGTACTATGGATCCTCTCAAGCA
genomic: AACTTTGGGTGCACCAACACTGTATGATCATCCTGGATCAGCCTATGGAAgtaagtcttt ... catcattcagGAGGGTACTATGGATCCTCTCAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgaaacttttctacaagacttggtatttcactgtttggctttcatcattcagGAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACGGATGACCTAAGACATTACTTTGGCAG
                                         ctttcatc  CT-rich tract
     aaactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctttgatctgttatagttttttttgtcagacttgaaacttttctacaagacttggtatttcactgtttggctttcatcattcagGAGGGTACTATGGATCCTCTCAAGCAGTGGGCAAGAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACGGATGACCTAAGACATTACTTTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA