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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgggcctggctcccctctcccccttccctcgccaatcgctcagatcccagggaccgacgcttgcgtgccgcttctccagatccctaaatctcacgccatttcttgaacccctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGCGTGTTTAGTTGCCCCATAGGCAAGAACCCCATGTACACCTACCGGGAGC

Basic information

species Zea mays
transcript GRMZM2G162292_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162292_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g38970.1 (Oryza sativa), 3'ss of exon 1
gtagtgggcctggctcccctctcccccttccctcgccaatcgctcagatcccagggaccgacgcttgcgtgccg--cttctccagatccc--taa------------atctcacgccatttcttg----aacccctcaa---cgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGCGTGTTTAGTTGCCCCATAGGCAAGAACCCCATGTACACCTACCGGGAGC
||      ||  ||  ||  |     |  |||| |  |   || ||  | |    |     |  | || | ||   || ||||||||| |  | |             |||| |||| ||| |||     | |||  |    ||||||||||||||||||| ||||||||||||||||||||||||  |||||||||||| || || |||||||| || ||||||||||||||||||||||| ||| 
gttcgcctccgcgcggcctcccagatcccccctagtgaggggcgcatttgcttttgcttcgccttcgccttccttcctcctccagatctcgctgattttggttggttctctctcgcccttttttgttcggatcccggaggtgcgcagGTCTATGGCGAGGAGGAGTGGTCGTTCGGGTTCTGCGAGAACGGCAGCGGCGTCTTCAGCTGCCCCATCGGGAAGAACCCCATGTACACCTACCGCGAGT
















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|211458568|gb|FL265854.1|FL265854
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211458574|gb|FL265860.1|FL265860
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|20507385|gb|BQ279606.1|BQ279606
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGTGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|148946992|gb|EC892286.2|EC892286
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211458579|gb|FL265865.1|FL265865
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAG
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAG
EST: gi|26456562|gb|CA828145.1|CA828145
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|74244398|gb|DT652312.1|DT652312
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|71436670|gb|DR817720.1|DR817720
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211458570|gb|FL265856.1|FL265856
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|148955405|gb|EC900974.2|EC900974
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211461090|gb|FL265868.1|FL265868
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|26456759|gb|CA828342.1|CA828342
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|37416464|gb|CF645882.1|CF645882
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|76281802|gb|DV021370.1|DV021370
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211458569|gb|FL265855.1|FL265855
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211355383|gb|FL265849.1|FL265849
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACG
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACG
EST: gi|211458581|gb|FL265867.1|FL265867
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211458573|gb|FL265859.1|FL265859
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|113701452|gb|EE678956.1|EE678956
EST:     CTTCCACAGCGCCGTGCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: CTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|20803170|gb|BQ294220.1|BQ294220
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211458578|gb|FL265864.1|FL265864
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|40303447|gb|CK347834.1|CK347834
EST:     CACAGCGCCGTGCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: CACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211355385|gb|FL265851.1|FL265851
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|148967884|gb|EE019185.2|EE019185
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|78080266|gb|DV508678.1|DV508678
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|76288414|gb|DV027982.1|DV027982
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|78105735|gb|DV524153.1|DV524153
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211355386|gb|FL265852.1|FL265852
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211458577|gb|FL265863.1|FL265863
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGT
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGT
EST: gi|74239047|gb|DT646961.1|DT646961
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211458576|gb|FL265862.1|FL265862
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|74236561|gb|DT644475.1|DT644475
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|78083904|gb|DV512297.1|DV512297
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211458572|gb|FL265858.1|FL265858
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
EST: gi|211458567|gb|FL265853.1|FL265853
EST:     TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAG                         GTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC
genomic: TCTTCAAGGACCGCATCGGCCTCGGCGGCATCTTCCACAGCGCCGTCCAGgtagtgggcc ... ctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccgcttctccagatccctaaatctcacgccatttcttgaacccctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGCGTGTTTAGTTGCCCCATAGGCAAGAACCCCATGTACACCTACCGGGAGC
                      atctcac  putative branch site (score: 3)
                                          cccctc  putative PPT
                   taaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgggcctggctcccctctcccccttccctcgccaatcgctcagatcccagggaccgacgcttgcgtgccgcttctccagatccctaaatctcacgccatttcttgaacccctcaacgcagGTCTATGGCGAGGACGAGTGGTCGTTCGGGTTCTGCGAGTCCGGCAGCGGCGTGTTTAGTTGCCCCATAGGCAAGAACCCCATGTACACCTACCGGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC