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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacagatggttttagtagtgctcatgtcacttgtctgtcttaatttttcatcatagtgggctgttattttggtgcattctcatgctaagtttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG

Basic information

species Zea mays
transcript GRMZM2G128121_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128121_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 10
---tgacagatggttttagtagtgctcatgtcacttgtctgtcttaatttttcatcatagtgggctgttattttggtgcattctcatgctaagtttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
   |    || | ||| |||||| |    |  ||||       || |  ||| || || |     | ||| |||  |   |||| ||||| | |||  ||||||| ||||| ||| ||||||| ||||||||||||||||||
tgctatttgaggttttaagtagtaccagcggtacttaaaatctttcacattt-atgattgcaa--tattacttttctatgttcttatgctcaatttttttcagGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG

upper sequence: GRMZM2G128121_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G36540.3 (Glycine max), 3'ss of exon 10
-tgacagatggttttagtagtgctcatgtcacttgtctgtcttaatttt---tcatcatagtgggctgttattttggtgcattctcatgctaagtttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
 | | | |     |||  |      ||   |  | |||| |    || |     | || |||||      ||| |     ||       ||  ||    || ||||||| |||| |||| | |||||||||||||||||||||
tttataaagaaaattaaaaaaaaaaattcaaaatctctgacccctttctgtactaccaaagtggagaac-attcttaaatatctcttctcttggtg---tttagGCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG

upper sequence: GRMZM2G128121_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G02380.1 (Glycine max), 3'ss of exon 10
-----tgacagatggttttagtagtgctcatgtcacttgtctgtcttaatttttcatcatagtgggctgttattttggtgcattctcatgctaagtttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
     |   | ||  | |||  |    |         || |   |||| | |   | || ||| |      ||| |     ||       ||  ||    || ||||||| |||| |||| | |||||||||||||||||||||
tagcgttttatattttcttaaaaaaaattgaaatctctgacc-ccttactgtactaccaaagtagagaac-attcttaaatatctcttctcttggtg---tttagGCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG

upper sequence: GRMZM2G128121_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G46380.2 (Glycine max), 3'ss of exon 10
-----tgacagatggttttagtagtgctcatgtcacttgtctgtcttaatttttcatcatagtgggctgttattttggtgcattctcatgctaagtttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
     | | |  |  |||||  |    |         || |   |||  | |   | || ||| |      ||| |     ||       ||   |    || ||||||| |||| |||| | |||||||||||||||||||||
gcgttttatatttttttttaaaaaaaattgaaatctctgacc-cctttctgtactaccaaagtagagaac-attcttaaatatctcttctcttgatg---tttagGCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAG

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|78115877|gb|DV534265.1|DV534265
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|148971222|gb|EE022081.2|EE022081
EST:     GTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: GTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|110220018|gb|EC901916.1|EC901916
EST:     AGATGTTACCATTACTGCGTTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AGATGTTACCATTACTGCG-TTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|78104220|gb|DV522638.1|DV522638
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|24769217|gb|CA404346.1|CA404346
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|71325375|gb|DR799361.1|DR799361
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|93013442|gb|EB638962.1|EB638962
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|71331066|gb|DR802363.1|DR802363
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|32856323|gb|CD996004.1|CD996004
EST:     AAGATGTTACCATTACTGCATTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|211386006|gb|FL329690.1|FL329690
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|211417439|gb|FL345693.1|FL345693
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|71429465|gb|DR810515.1|DR810515
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|149109553|gb|EE293365.2|EE293365
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|60341592|gb|DN208565.1|DN208565
EST:     AAGATGTTACCATTACTGCGTTTTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|4730273|gb|AI649439.1|AI649439
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|78081841|gb|DV510253.1|DV510253
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|78180140|gb|DV550513.1|DV550513
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|12045820|gb|BF727959.1|BF727959
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|31348876|gb|CD433233.1|CD433233
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|76290822|gb|DV030390.1|DV030390
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|211179193|gb|FL462626.1|FL462626
EST:     GCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: GCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|76021492|gb|DT948662.1|DT948662
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|6859967|gb|AW355961.1|AW355961
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 335

ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 457

ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 416

ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 715

ATAGAACGTGGGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgccatg ... tttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcatcatagtgggctgttattttggtgcattctcatgctaagtttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
                                             tttgcttc  CT-rich tract
                 tgttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacagatggttttagtagtgctcatgtcacttgtctgtcttaatttttcatcatagtgggctgttattttggtgcattctcatgctaagtttgcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - gctcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgggctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgcta