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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtacgtacgagtgctgctacgtgaccttgtcgtcagttactttcagttaaattcttgcactgctgaagcacgtgtttgtttaagaggaatgctaatcgacttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG

Basic information

species Zea mays
transcript GRMZM2G146463_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146463_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g26900.1 (Oryza sativa), 3'ss of exon 3
gtagtacgtacgagtgctgctacgtgaccttgtcgtcagttactttcagttaaattcttgcactgctgaagcacgtgtttgtttaagaggaatgctaatcgacttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG
            || |     || ||  ||| ||       | |         ||   ||||||  |  | || |  | |||| || |  ||  ||  | || |      ||||| ||||| |  ||| | || ||||  ||||| || || || ||||| || |||||||| || ||||||||||||||||| || ||||| |||||||| |
-----------cagaggcataacatgtacttctccctgaacattaattaacttatcagtgcactcttctaacatgc-tatgttaaatattaacactctttgagt-atcatcagGGTTACATAGCTGCTGATCCAAAGAAGTTCCCTTCGGGGATTAAGGCACTCGCAGATTATGTGCACAGCAAGGGGCTTAAACTAGGCATATACTCTTCAG

upper sequence: GRMZM2G146463_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G44820.1 (Glycine max), 3'ss of exon 4
---gtagtacgtacgagtgct----gctacgtgac-cttgtcgtcagttactttcagttaaattcttgcactgctgaagcacgtgtttgtttaagaggaatgctaatcgact--tgctg----------acagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG
    | || | || |  |  |    ||| | |  |  |||   |   |||||  |    | |   ||       | ||  |  | ||| ||    |   ||  | || | ||  || ||          | ||||  |  |||| || ||       || || || || |||||||| || || |||||||| |||||| ||||||| ||||||||||| || || ||     
ggtatggttcttatggtttttacatgcttcattgcatttgaatttgcttactgcctcccagaaagttatcacattcaattaatttttttttcttcaaacatttttataggctattgttgttgtattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACGGCAAGGGTCTTAAGCTTGGAATTTATTCAGAT-

upper sequence: GRMZM2G146463_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G40990.1 (Glycine max), 3'ss of exon 4
--gtagtacgtacgagtgctgc-tacgtgaccttgtcgtcagttactttcagtt-------aaattcttgcact-gctgaagcacgtgtttgtttaagaggaatgctaatcgact--tgctg-------acagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG
   | || | || |  |  | | | | | |     |   || || ||| | ||        || ||||  || |   | ||     | ||| || ||      |  ||  | | |  || ||       | ||||  |  |||| || ||       ||||| || || |||||||| || || |||||||| |||||||||||||| ||||||||||| || || ||    |
gtatggttcttatggtttttacatgcttcattgcatttgcactttcttactgtctccttgaaagttctcacattcaattaaatttatttttcttcaaacatttttataggctattgttgttgtattgctatagGGTAATCTGGTAGCAAAAAAATCAACATTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACAGCAAGGGTCTTAAGCTTGGAATTTATTCAGATG

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|211092681|gb|FL286914.1|FL286914
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|76930345|gb|DV172346.1|DV172346
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|89250668|gb|DY622454.1|DY622454
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|78113279|gb|DV531671.1|DV531671
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|91054335|gb|EB164753.1|EB164753
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|211092689|gb|FL286922.1|FL286922
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGA
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGA
EST: gi|211095153|gb|FL286926.1|FL286926
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAR                         GGATACATGGTCGCTAACCCCAAGA
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGA
EST: gi|211095154|gb|FL286927.1|FL286927
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|71431665|gb|DR812715.1|DR812715
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|78108215|gb|DV526633.1|DV526633
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|149055656|gb|EE156361.2|EE156361
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|101386530|gb|EB815281.1|EB815281
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|71442888|gb|DR823938.1|DR823938
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGGCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|78075209|gb|DV503643.1|DV503643
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG                         T
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-Ggtagtacgta ... ttgctgacag-
EST: gi|78075209|gb|DV503643.1|DV503643
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG                         T
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-Ggtagtacgta ... ttgctgacag-
EST: gi|78075209|gb|DV503643.1|DV503643
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG                         T
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-Ggtagtacgta ... ttgctgacag-
EST: gi|71442889|gb|DR823939.1|DR823939
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|71435988|gb|DR817038.1|DR817038
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|78088431|gb|DV516824.1|DV516824
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|29947680|gb|CB816781.1|CB816781
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|211095152|gb|FL286925.1|FL286925
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGC
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGC
EST: gi|71428787|gb|DR809837.1|DR809837
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|37424719|gb|CF650092.1|CF650092
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|211092683|gb|FL286916.1|FL286916
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCA
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCA
EST: gi|71443418|gb|DR824468.1|DR824468
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|71443280|gb|DR824330.1|DR824330
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|71318127|gb|DR795825.1|DR795825
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|148940241|gb|EC885013.2|EC885013
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|91875282|gb|EB405239.1|EB405239
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|74238712|gb|DT646626.1|DT646626
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|76011884|gb|DT939054.1|DT939054
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|149009677|gb|EE041609.2|EE041609
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|78110547|gb|DV528957.1|DV528957
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|148973153|gb|EE024223.2|EE024223
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|211092685|gb|FL286918.1|FL286918
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|149013904|gb|EE043402.2|EE043402
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|89763957|gb|DY690934.1|DY690934
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|50334852|gb|CO529978.1|CO529978
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAG                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGgtagtacgta ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcactgctgaagcacgtgtttgtttaagaggaatgctaatcgacttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG
                                  tgctaat  putative branch site (score: 2)
                   tttgtttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtacgtacgagtgctgctacgtgaccttgtcgtcagttactttcagttaaattcttgcactgctgaagcacgtgtttgtttaagaggaatgctaatcgacttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG