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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacgagtgctgctacgtgaccttgtcgtcagttactttcagttaaattcttgcactgctgaagcacgtgtttgtttaagaggaatgctaatcgacttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG

Basic information

species Zea mays
transcript GRMZM2G146463_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146463_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g26900.1 (Oryza sativa), 3'ss of exon 3
gtacgtacgagtgctgctacgtgaccttgtcgtcagttactttcagttaaattcttgcactgctgaagcacgtgtttgtttaagaggaatgctaatcgacttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG
         || |     || ||  ||| ||       | |         ||   ||||||  |  | || |  | |||| || |  ||  ||  | || |      ||||| ||||| |  ||| | || ||||  ||||| || || || ||||| || |||||||| || ||||||||||||||||| || ||||| |||||||| |
--------cagaggcataacatgtacttctccctgaacattaattaacttatcagtgcactcttctaacatgc-tatgttaaatattaacactctttgagt-atcatcagGGTTACATAGCTGCTGATCCAAAGAAGTTCCCTTCGGGGATTAAGGCACTCGCAGATTATGTGCACAGCAAGGGGCTTAAACTAGGCATATACTCTTCAG

upper sequence: GRMZM2G146463_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G44820.1 (Glycine max), 3'ss of exon 4
------gtacgtacgagtgct----gctacgtgac-cttgtcgtcagttactttcagttaaattcttgcactgctgaagcacgtgtttgtttaagaggaatgctaatcgact--tgctg----------acagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG
      || | || |  |  |    ||| | |  |  |||   |   |||||  |    | |   ||       | ||  |  | ||| ||    |   ||  | || | ||  || ||          | ||||  |  |||| || ||       || || || || |||||||| || || |||||||| |||||| ||||||| ||||||||||| || || ||     
ggtatggttcttatggtttttacatgcttcattgcatttgaatttgcttactgcctcccagaaagttatcacattcaattaatttttttttcttcaaacatttttataggctattgttgttgtattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACGGCAAGGGTCTTAAGCTTGGAATTTATTCAGAT-

upper sequence: GRMZM2G146463_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G40990.1 (Glycine max), 3'ss of exon 4
-----gtacgtacgagtgctgc-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|78108215|gb|DV526633.1|DV526633
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|71428787|gb|DR809837.1|DR809837
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|37424719|gb|CF650092.1|CF650092
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|50334852|gb|CO529978.1|CO529978
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|71443418|gb|DR824468.1|DR824468
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|148973153|gb|EE024223.2|EE024223
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|91875282|gb|EB405239.1|EB405239
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|91054335|gb|EB164753.1|EB164753
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|211092688|gb|FL286921.1|FL286921
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|89763957|gb|DY690934.1|DY690934
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|71435988|gb|DR817038.1|DR817038
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|29947680|gb|CB816781.1|CB816781
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|71443280|gb|DR824330.1|DR824330
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|74238712|gb|DT646626.1|DT646626
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|149009677|gb|EE041609.2|EE041609
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|78113279|gb|DV531671.1|DV531671
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|148940241|gb|EC885013.2|EC885013
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|78075209|gb|DV503643.1|DV503643
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTA                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|89250668|gb|DY622454.1|DY622454
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|71318127|gb|DR795825.1|DR795825
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|76011884|gb|DT939054.1|DT939054
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|71442888|gb|DR823938.1|DR823938
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGGCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|78088431|gb|DV516824.1|DV516824
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|149013904|gb|EE043402.2|EE043402
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|78110547|gb|DV528957.1|DV528957
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|211095154|gb|FL286927.1|FL286927
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|71431665|gb|DR812715.1|DR812715
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|149055656|gb|EE156361.2|EE156361
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGA-G--                         GGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|71442889|gb|DR823939.1|DR823939
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
EST: gi|76930345|gb|DV172346.1|DV172346
EST:     ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGG--                         G-ATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG
genomic: ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 29

ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 27

ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG


Block sizes: 48 (upstream exon), 33 (downstream exon)
Score: 10

ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG


Block sizes: 45 (upstream exon), 33 (downstream exon)
Score: 9

ATGACTGCTGGGCGGATTCCGAGAGAACCAAAGAGGTAgtacgtacga ... ttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcactgctgaagcacgtgtttgtttaagaggaatgctaatcgacttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG
                                  tgctaat  putative branch site (score: 9)
                   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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtacgagtgctgctacgtgaccttgtcgtcagttactttcagttaaattcttgcactgctgaagcacgtgtttgtttaagaggaatgctaatcgacttgctgacagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG

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