Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagcagaaaagatcaagaggtccttgaactgttatgctgttcttttagttacccttccttcaacagagcaagttttgaactcagcccaaaacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATAC

Basic information

species Zea mays
transcript GRMZM2G121452_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121452_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g25420.2 (Oryza sativa), 3'ss of exon 2
-gtagcagaaaagatcaagaggtccttgaactgttatgctgttcttttagttacccttccttcaacagagcaagttttgaactcagcccaaaacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATAC
  |  || |    ||       |  || |||||| ||     |  |    |||   |  | |  ||    | |||  | |  | |      ||  ||||||||||||| ||||||||||| |||||| ||||||||||| |||| ||||||||||| |||||| | || || || || || || |||||||||||||||||
attcccacagtgaatttcactttaattaaactgt-ataacaataataagattaaaatagccttcacctgtctagtactaagataaatgtgtaatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAGATGCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATAC

upper sequence: GRMZM2G121452_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G25730.1 (Glycine max), 3'ss of exon 2
gtagcagaaaagatcaagaggtccttgaactgttat--gctgttcttttagttacccttccttcaacagagcaagttttga--actcagcccaaaacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATAC
     |   |  ||||| | |    |      ||||    ||      ||   |   ||     | ||     | ||||      |        ||  || ||||||| || || ||||||||||||||  | |||||||||  |||||| |||||||| |||||| | ||||||| |||| ||||||||||||| |  ||| |
----tatttagtatcaataagattatagctacttattaaatgaaaaagtaaaaaatgttaagatatcaagtttattttttcctgttggttttttaaacttccagGGGATATATACGAGCATGCTGTTGTCCTTAGTGTGAAAAATGAGGATCAAGATGCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGC

upper sequence: GRMZM2G121452_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G08690.1 (Glycine max), 3'ss of exon 2
gtagcagaaaagat-caagaggtccttgaactgttatgctgttcttttagttacccttccttcaacagagcaagttttgaactcagcccaaaacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATAC
 |||||  || ||   || |  | |||      | |    ||       ||||    |  |    |  ||    ||||    |  |     ||  || ||||||| || |||||||||||||||||  | ||||||||| ||||||| |||||||| || ||| | ||||||| |||| ||||||||||||| |  ||| |
-tagcatcaatgagataatatctacttattaaatgaaaaggtaaaaaatgttagaagttttatgtctaagttttttttcctgttggtttttaaacttccagGGGATATATATGAGCATGCTGTTGTCCTTAGTGTGAAAATTGAGGATCAAGATGCTTTCGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGC

upper sequence: GRMZM2G121452_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G64520.1 (Arabidopsis thaliana), 3'ss of exon 2
gtagcagaaaagatcaagaggtccttgaactgttatgctgttcttt-tagttacccttcct-tcaacagagcaagttttgaactcagccca---aaacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATAC
     |  ||   |  |  | | | |    |   ||   ||| ||  || ||    ||| | |  |     |   | |  ||||  | | |       |||  |||||||||||||||||||||||||||| | || || |||   ||||| |||||||| |||||  | ||||||| ||||||||| ||||| ||  ||||| |
-----attaatcgttgaatgctgcattggtttggattgagttattggtaatttttgttcttattgattatccgtttctaaaactttgacaattggtgtattctagGGGACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGC

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|50322448|gb|CO517574.1|CO517574
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|31350060|gb|CD434417.1|CD434417
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|28873350|gb|CB329351.1|CB329351
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|71314411|gb|DR793830.1|DR793830
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|76925420|gb|DV170446.1|DV170446
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|211061321|gb|FL214580.1|FL214580
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|60346094|gb|DN213067.1|DN213067
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|211061319|gb|FL214578.1|FL214578
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|71421223|gb|DR805346.1|DR805346
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|76290008|gb|DV029576.1|DV029576
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|91877590|gb|EB407547.1|EB407547
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|71447603|gb|DR828653.1|DR828653
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGAACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|74245478|gb|DT653392.1|DT653392
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAG                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|32910063|gb|CF014875.1|CF014875
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|76285525|gb|DV025093.1|DV025093
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|15208703|gb|BI430587.1|BI430587
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGT
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGT
EST: gi|211061322|gb|FL214581.1|FL214581
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|4152193|gb|AI372327.1|AI372327
EST:     CAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: CAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|211374252|gb|FL175468.1|FL175468
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|211061318|gb|FL214577.1|FL214577
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|50324364|gb|CO519490.1|CO519490
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|32919291|gb|CF024103.1|CF024103
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|76909132|gb|DV163238.1|DV163238
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|50323893|gb|CO519019.1|CO519019
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGGTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|28873669|gb|CB329625.1|CB329625
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|71444673|gb|DR825723.1|DR825723
EST:     CAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: CAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|32912839|gb|CF017651.1|CF017651
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|89251271|gb|DY623057.1|DY623057
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|31351657|gb|CD436014.1|CD436014
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|91049533|gb|EB159951.1|EB159951
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|76015137|gb|DT942307.1|DT942307
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|88751295|gb|DY535436.1|DY535436
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAG                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|93282632|gb|EB674896.1|EB674896
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|33091534|gb|CF051528.1|CF051528
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|211058357|gb|FL214575.1|FL214575
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
EST: gi|31355614|gb|CD439971.1|CD439971
EST:     GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAA                         GGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG
genomic: GCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAG

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: 49 (upstream exon), 49 (downstream exon)
Score: 207

GTCCATCTCACCCAATTCCCCAGCCTTCCGCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

GTCCATCTCACCCAATTCCCCAGCCTTCCGCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

GTCCATCTCACCCAATTCCCCAGCCTTCCGCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATAC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 84

GTCCATCTCACCCAATTCCCCAGCCTTCCGCCCTTGTTTCAGCAGACACCGAACATTGTGGAGGAGCTCAAACTTGCAAgtaagatggc ... aacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttacccttccttcaacagagcaagttttgaactcagcccaaaacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATAC
                                           aaaacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcagaaaagatcaagaggtccttgaactgttatgctgttcttttagttacccttccttcaacagagcaagttttgaactcagcccaaaacatttcagGGGACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
gtagcag
- - - -aaaagatc
- - - - - - - - - - - - -tgaactg
- - - - - - - - - - - - - - - - -tatgctg